Revolutionizing Genomics with Genome Graphs
Genome graphs represent a revolutionary advancement in genomics, moving beyond linear reference genomes to encompass the vast diversity of genomic variation within populations. These complex data structures integrate multiple genome sequences, enabling more accurate and comprehensive analysis of genetic information. Applications range from improving disease diagnostics to facilitating more effective personalized medicine, as genome graphs provide a richer context for understanding individual genetic differences and their implications for health. This technology offers significant potential for advancing biological and medical research.
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"sequence" : "ACGTACGTAGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGTTTACGTACGTAAACCCGGGTTTACGTAC",
"trace" : {
"A" : [4,9,22,56,123,228,357,467,510,467,357,228,123,56,22,9,4,5,12,25,45,70,91,100,91,70,45,25,12,5,11,24,43,67,87,95,87,67,43,24,11,3,4,7,14,27,49,76,99,108,99,76,49,27,14,7,4,3,57,125,233,364,475,520,475,364,233,125,57,16,30,51,78,101,110,101,78,51,30,16,4,6,12,25,44,68,88,96,88,68,44,25,12,6,4,6,12,26,47,73,95,104,95,73,47,26,12,6,55,117,216,337,440,481,440,337,216,117,55,5,11,24,43,67,87,95,87,67,43,24,11,5,4,5,8,14,28,50,76,98,107,98,76,50,28,14,8,5,4,22,57,127,236,370,484,529,484,370,236,127,57,22,50,111,208,325,426,466,426,325,208,111,50,24,57,122,225,350,457,500,457,350,225,122,57,24,2,4,11,24,45,70,92,100,92,70,45,24,11,4,2,1,2,5,11,25,47,73,96,105,96,73,47,25,11,5,2,1,14,28,50,76,99,108,99,76,50,28,14,8,14,28,50,76,99,108,99,76,50,28,14,8,3,5,11,23,42,65,84,92,84,65,42,23,11,5,3,7,14,28,50,76,99,108,99,76,50,28,14,7,4,6,13,26,46,70,91,100,91,70,46,26,13,6,4,2,4,10,22,41,64,84,92,84,64,41,22,10,4,2,11,23,43,67,88,96,88,67,43,23,11,24,60,131,244,381,498,544,498,381,244,131,60,24,1,2,5,12,26,49,77,101,110,101,77,49,26,12,5,2,1,6,12,26,47,73,95,104,95,73,47,26,12,6,2,4,10,22,41,64,84,92,84,64,41,22,10,4,2,53,117,217,339,443,485,443,339,217,117,53,1,2,5,12,26,49,76,100,109,100,76,49,26,12,5,2,1,5,12,26,49,76,100,109,100,76,49,26,12,5,5,8,15,28,50,77,99,108,99,77,50,28,15,8,5,51,112,207,324,423,463,423,324,207,112,51,18,48,108,203,318,416,455,416,318,203,108,48,18,10,23,53,114,209,326,426,465,426,326,209,114,53,23,10,2,4,10,22,41,64,83,91,83,64,41,22,10,4,2,1,2,5,12,27,49,77,101,110,101,77,49,27,12,5,2,1,12,24,43,67,87,95,87,67,43,24,12,8,15,29,51,78,101,110,101,78,51,29,15,8,1,2,4,11,24,44,69,90,98,90,69,44,24,11,4,2,1,15,28,50,77,100,109,100,77,50,28,15,1,2,4,11,24,44,69,90,99,90,69,44,24,11,4,2,1,4,7,14,28,51,79,102,112,102,79,51,28,14,7,4,4,7,13,27,48,74,97,105,97,74,48,27,13,7,4,4,9,24,60,131,244,381,498,545,498,381,244,131,60,24,9,4,15,27,47,71,92,100,92,71,47,27,15,15,28,50,76,99,108,99,76,50,28,15,6,9,16,30,52,79,102,111,102,79,52,30,16,9,6,6,18,48,108,202,317,415,454,415,317,202,108,48,18,6,2,3,6,13,27,49,76,99,108,99,76,49,27,13,6,3,2,9,16,30,53,81,104,114,104,81,53,30,16,9,3,6,12,26,47,73,95,104,95,73,47,26,12,6,3,2,6,19,51,115,215,336,440,482,440,336,215,115,51,19,6,2,11,25,59,128,236,368,481,526,481,368,236,128,59,25,11,8,22,55,123,229,358,469,513,469,358,229,123,55,22,8,6,13,27,49,76,98,108,98,76,49,27,13,6,5,12,26,49,76,99,108,99,76,49,26,12,5,3,6,13,27,50,77,100,110,100,77,50,27,13,6,3,12,25,45,70,91,99,91,70,45,25,12,3,5,12,25,45,69,90,99,90,69,45,25,12,5,3,12,24,44,69,90,98,90,69,44,24,12,3,4,7,13,27,49,75,97,106,97,75,49,27,13,7,4,3,5,8,14,28,50,76,99,108,99,76,50,28,14,8,5,55,122,227,356,466,509,466,356,227,122,55,3,6,12,26,48,74,97,106,97,74,48,26,12,6,3,13,27,48,73,95,104,95,73,48,27,13,3,4,7,14,27,49,76,99,108,99,76,49,27,14,7,4,3,6,11,26,61,132,243,379,495,541,495,379,243,132,61,26,11,6,14,27,46,69,89,97,89,69,46,27,14,4,11,24,45,71,93,101,93,71,45,24,11,4,2,3,6,13,27,50,77,100,110,100,77,50,27,13,6,3,2,2,7,20,53,118,222,348,456,499,456,348,222,118,53,20,7,2,3,8,22,58,128,240,375,491,537,491,375,240,128,58,22,8,3,6,18,49,109,204,320,420,459,420,320,204,109,49,18,6,4,10,22,41,64,83,91,83,64,41,22,10,4,3,6,13,28,50,78,102,111,102,78,50,28,13,6,3,5,12,25,45,70,91,100,91,70,45,25,12,5,6,8,15,28,49,74,95,103,95,74,49,28,15,8,6,12,25,45,70,91,100,91,70,45,25,12,6,13,26,48,75,97,106,97,75,48,26,13,6,5,12,26,48,75,98,107,98,75,48,26,12,5,3,4,6,12,24,43,67,86,94,86,67,43,24,12,6,4,3,9,15,29,50,76,98,107,98,76,50,29,15,9,6,11,26,61,132,243,379,495,541,495,379,243,132,61,26,11,6,2,5,12,25,47,73,96,105,96,73,47,25,12,5,2,8,15,29,52,79,103,112,103,79,52,29,15,8,3,6,12,26,47,73,95,104,95,73,47,26,12,6,3,9,22,56,122,227,354,463,506,463,354,227,122,56,22,9,4,6,13,26,46,70,91,100,91,70,46,26,13,6,4],
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"sequence" : "AAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAAC",
"trace" : {
"A" : [6,18,49,109,203,319,417,457,417,319,203,109,49,18,6,2,6,19,50,112,210,330,432,472,432,330,210,112,50,19,6,2,5,10,23,57,124,230,359,469,513,469,359,230,124,57,23,10,5,13,27,48,74,96,105,96,74,48,27,13,5,11,23,42,65,85,93,85,65,42,23,11,5,2,4,11,24,45,70,91,100,91,70,45,24,11,4,2,11,24,44,69,90,98,90,69,44,24,11,6,13,28,50,78,102,111,102,78,50,28,13,6,12,26,49,76,100,109,100,76,49,26,12,2,4,11,24,45,70,91,100,91,70,45,24,11,4,2,2,4,10,23,42,66,86,94,86,66,42,23,10,4,2,1,2,4,11,24,46,71,93,102,93,71,46,24,11,4,2,1,3,8,21,55,122,228,357,468,512,468,357,228,122,55,21,8,3,15,28,49,75,96,105,96,75,49,28,15,1,2,5,11,25,46,72,95,104,95,72,46,25,11,5,2,1,6,13,26,48,75,98,107,98,75,48,26,13,6,7,22,58,130,243,381,499,546,499,381,243,130,58,22,7,4,6,12,24,43,65,85,93,85,65,43,24,12,6,4,5,12,26,48,75,98,107,98,75,48,26,12,5,2,4,11,24,44,68,89,98,89,68,44,24,11,4,2,24,58,125,230,358,468,512,468,358,230,125,58,24,50,109,203,317,414,453,414,317,203,109,50,8,22,54,119,220,344,450,492,450,344,220,119,54,22,8,4,10,23,42,65,86,94,86,65,42,23,10,4,5,12,26,48,75,99,108,99,75,48,26,12,5,9,16,29,51,78,100,109,100,78,51,29,16,9,3,4,6,13,25,45,69,90,98,90,69,45,25,13,6,4,3,1,2,5,12,26,48,74,97,106,97,74,48,26,12,5,2,1,3,5,11,23,42,65,84,92,84,65,42,23,11,5,3,4,5,7,14,27,48,73,95,103,95,73,48,27,14,7,5,4,15,28,49,74,95,104,95,74,49,28,15,15,28,48,73,94,103,94,73,48,28,15,5,9,22,54,116,215,336,439,480,439,336,215,116,54,22,9,5,11,24,45,70,91,99,91,70,45,24,11,7,14,27,48,73,95,103,95,73,48,27,14,7,2,3,5,12,25,45,70,91,100,91,70,45,25,12,5,3,2,23,59,132,246,385,504,551,504,385,246,132,59,23,11,23,43,66,86,94,86,66,43,23,11,7,14,27,49,76,99,108,99,76,49,27,14,7,1,2,5,12,26,49,76,100,109,100,76,49,26,12,5,2,1,50,113,211,331,433,474,433,331,211,113,50,2,7,20,54,120,225,352,461,505,461,352,225,120,54,20,7,2,7,21,56,125,234,366,480,525,480,366,234,125,56,21,7,9,15,29,50,76,99,108,99,76,50,29,15,9,16,30,52,79,103,112,103,79,52,30,16,13,25,44,67,87,95,87,67,44,25,13,7,14,28,51,78,102,111,102,78,51,28,14,7,2,4,10,22,41,64,84,92,84,64,41,22,10,4,2,2,4,11,23,43,67,88,96,88,67,43,23,11,4,2,5,7,13,25,45,68,88,96,88,68,45,25,13,7,5,4,5,8,15,28,50,76,99,108,99,76,50,28,15,8,5,4,15,27,47,71,92,100,92,71,47,27,15,7,21,56,125,235,368,482,528,482,368,235,125,56,21,7,6,12,25,44,68,88,96,88,68,44,25,12,6,2,3,5,11,23,42,66,85,93,85,66,42,23,11,5,3,2,2,4,10,22,41,65,85,93,85,65,41,22,10,4,2,4,8,22,54,118,220,343,448,490,448,343,220,118,54,22,8,4,13,26,45,69,90,98,90,69,45,26,13,4,5,8,15,30,52,80,104,113,104,80,52,30,15,8,5,4,2,3,6,13,27,49,76,99,108,99,76,49,27,13,6,3,2,9,23,55,120,222,347,453,496,453,347,222,120,55,23,9,60,131,243,380,496,543,496,380,243,131,60,11,26,61,132,244,380,496,542,496,380,244,132,61,26,11,2,4,11,24,44,69,90,98,90,69,44,24,11,4,2,4,11,24,45,70,91,100,91,70,45,24,11,4,8,15,28,48,73,94,103,94,73,48,28,15,8,12,26,47,74,96,105,96,74,47,26,12,5,6,9,15,29,51,77,99,108,99,77,51,29,15,9,6,5,3,5,11,23,42,66,86,94,86,66,42,23,11,5,3,4,5,7,14,26,47,71,92,100,92,71,47,26,14,7,5,4,5,8,15,29,52,79,102,112,102,79,52,29,15,8,5,5,6,9,16,30,53,80,104,113,104,80,53,30,16,9,6,5,20,50,110,204,318,416,455,416,318,204,110,50,20,11,25,46,72,94,103,94,72,46,25,11,3,4,6,13,26,46,71,93,101,93,71,46,26,13,6,4,3,13,27,50,77,101,110,101,77,50,27,13,60,132,245,383,501,548,501,383,245,132,60,13,27,50,77,101,110,101,77,50,27,13,10,23,42,66,86,95,86,66,42,23,10,4,6,12,25,44,67,87,95,87,67,44,25,12,6,4,58,129,242,380,498,544,498,380,242,129,58,6,18,49,109,204,320,419,458,419,320,204,109,49,18,6,23,57,125,232,362,474,518,474,362,232,125,57,23,4,5,8,15,29,52,80,103,112,103,80,52,29,15,8,5,4],
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"sequence" : "TAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCGGGTTTACGTACGTAAACCG",
"trace" : {
"A" : [3,5,12,25,45,70,92,100,92,70,45,25,12,5,3,4,9,23,59,129,240,374,489,535,489,374,240,129,59,23,9,4,8,21,51,112,209,326,427,467,427,326,209,112,51,21,8,21,55,123,231,363,475,519,475,363,231,123,55,21,12,26,48,74,97,106,97,74,48,26,12,1,2,5,11,25,46,73,95,104,95,73,46,25,11,5,2,1,5,12,26,49,77,100,109,100,77,49,26,12,5,12,26,48,75,98,107,98,75,48,26,12,2,4,10,22,42,65,85,93,85,65,42,22,10,4,2,14,26,45,68,87,95,87,68,45,26,14,15,28,48,73,95,103,95,73,48,28,15,1,2,5,12,26,48,75,98,107,98,75,48,26,12,5,2,1,16,29,51,78,101,110,101,78,51,29,16,2,7,20,53,119,223,349,457,500,457,349,223,119,53,20,7,2,12,25,47,74,96,105,96,74,47,25,12,6,13,25,46,70,91,99,91,70,46,25,13,6,4,7,14,28,49,76,99,108,99,76,49,28,14,7,4,20,52,117,220,345,451,494,451,345,220,117,52,20,7,14,27,48,74,95,104,95,74,48,27,14,7,8,15,29,52,79,102,112,102,79,52,29,15,8,12,25,44,68,88,96,88,68,44,25,12,7,21,54,122,228,358,469,513,469,358,228,122,54,21,7,54,117,218,340,445,487,445,340,218,117,54,49,109,204,319,417,456,417,319,204,109,49,5,7,14,27,48,73,94,103,94,73,48,27,14,7,5,15,27,47,71,92,100,92,71,47,27,15,1,2,4,10,22,41,65,85,93,85,65,41,22,10,4,2,1,6,13,27,50,78,102,111,102,78,50,27,13,6,11,24,45,70,91,100,91,70,45,24,11,5,11,24,43,67,87,95,87,67,43,24,11,5,8,14,26,45,68,88,96,88,68,45,26,14,8,12,26,47,72,94,103,94,72,47,26,12,7,13,26,45,69,89,97,89,69,45,26,13,7,4,9,24,59,130,243,379,496,543,496,379,243,130,59,24,9,4,15,29,52,80,103,113,103,80,52,29,15,4,7,14,28,51,78,102,111,102,78,51,28,14,7,4,12,26,48,75,98,107,98,75,48,26,12,23,57,123,228,356,466,509,466,356,228,123,57,23,12,26,48,74,97,105,97,74,48,26,12,8,15,27,47,71,92,100,92,71,47,27,15,8,14,28,49,75,98,106,98,75,49,28,14,56,121,224,350,458,500,458,350,224,121,56,9,21,52,112,208,324,423,463,423,324,208,112,52,21,9,2,7,20,54,120,225,353,463,506,463,353,225,120,54,20,7,2,3,4,6,13,26,46,71,92,100,92,71,46,26,13,6,4,3,4,5,7,13,25,44,68,88,95,88,68,44,25,13,7,5,4,4,6,12,25,45,69,89,97,89,69,45,25,12,6,4,1,2,4,10,22,42,65,85,93,85,65,42,22,10,4,2,1,11,24,43,67,87,95,87,67,43,24,11,4,11,23,43,68,89,97,89,68,43,23,11,4,5,6,9,16,30,53,81,104,114,104,81,53,30,16,9,6,5,12,25,44,68,88,97,88,68,44,25,12,14,29,51,79,103,112,103,79,51,29,14,10,24,59,128,237,370,483,528,483,370,237,128,59,24,10,8,15,29,51,77,100,109,100,77,51,29,15,8,15,29,51,77,99,108,99,77,51,29,15,4,6,12,24,43,66,85,93,85,66,43,24,12,6,4,23,56,119,220,343,447,489,447,343,220,119,56,23,7,13,25,45,68,88,96,88,68,45,25,13,7,8,15,28,48,73,94,102,94,73,48,28,15,8,8,14,26,45,68,87,95,87,68,45,26,14,8,4,8,21,52,114,211,330,431,472,431,330,211,114,52,21,8,4,23,58,128,239,373,488,534,488,373,239,128,58,23,11,25,59,127,234,365,476,521,476,365,234,127,59,25,11,3,6,13,27,50,78,101,111,101,78,50,27,13,6,3,5,7,14,28,49,74,96,105,96,74,49,28,14,7,5,11,23,42,65,84,92,84,65,42,23,11,6,13,27,48,75,98,107,98,75,48,27,13,6,4,5,7,14,27,48,74,96,104,96,74,48,27,14,7,5,4,5,7,13,25,44,68,87,95,87,68,44,25,13,7,5,6,8,15,28,49,75,96,105,96,75,49,28,15,8,6,1,2,4,11,23,44,68,89,97,89,68,44,23,11,4,2,1,5,10,25,61,133,246,384,502,548,502,384,246,133,61,25,10,5,2,3,5,11,24,43,67,87,95,87,67,43,24,11,5,3,2,4,5,7,13,25,44,68,88,95,88,68,44,25,13,7,5,4,4,11,24,45,71,93,101,93,71,45,24,11,4,57,124,231,361,472,517,472,361,231,124,57,3,4,7,13,27,49,75,97,106,97,75,49,27,13,7,4,3,1,2,5,11,25,46,72,94,103,94,72,46,25,11,5,2,1,5,12,25,46,72,94,102,94,72,46,25,12,5,51,112,208,326,427,467,427,326,208,112,51,58,126,233,363,475,519,475,363,233,126,58,53,113,208,324,423,462,423,324,208,113,53,11,25,46,73,95,104,95,73,46,25,11,2,4,10,22,42,65,85,93,85,65,42,22,10,4,2,12,25,46,71,93,101,93,71,46,25,12],
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"A" : [14,26,46,70,91,99,91,70,46,26,14,6,12,26,47,74,96,105,96,74,47,26,12,6,4,10,23,43,67,87,95,87,67,43,23,10,4,4,10,22,42,65,85,93,85,65,42,22,10,4,13,26,48,73,95,104,95,73,48,26,13,6,9,16,30,52,78,101,111,101,78,52,30,16,9,6,13,26,46,71,92,101,92,71,46,26,13,1,2,4,11,24,45,70,92,100,92,70,45,24,11,4,2,1,52,115,213,332,435,475,435,332,213,115,52,4,5,7,13,25,44,67,87,95,87,67,44,25,13,7,5,4,13,27,49,77,100,109,100,77,49,27,13,6,12,25,44,68,88,96,88,68,44,25,12,6,24,60,130,242,377,493,539,493,377,242,130,60,24,12,25,44,68,89,97,89,68,44,25,12,4,7,13,27,48,74,96,105,96,74,48,27,13,7,4,4,6,13,25,45,69,90,98,90,69,45,25,13,6,4,3,7,21,53,117,218,341,446,488,446,341,218,117,53,21,7,3,9,23,58,127,237,370,483,529,483,370,237,127,58,23,9,57,123,228,355,464,508,464,355,228,123,57,3,5,12,26,47,73,95,103,95,73,47,26,12,5,3,4,10,22,41,64,84,92,84,64,41,22,10,4,10,22,41,63,83,91,83,63,41,22,10,1,2,4,10,22,41,64,83,91,83,64,41,22,10,4,2,1,4,5,8,14,28,50,76,99,108,99,76,50,28,14,8,5,4,4,6,13,25,45,70,90,99,90,70,45,25,13,6,4,10,22,41,64,84,92,84,64,41,22,10,4,11,24,44,69,90,99,90,69,44,24,11,4,3,6,12,26,48,74,97,105,97,74,48,26,12,6,3,52,116,216,338,443,484,443,338,216,116,52,5,6,8,15,29,50,76,98,107,98,76,50,29,15,8,6,5,5,11,25,46,72,94,103,94,72,46,25,11,5,11,25,46,72,94,103,94,72,46,25,11,10,23,56,121,223,348,455,498,455,348,223,121,56,23,10,2,3,6,13,27,50,77,100,109,100,77,50,27,13,6,3,2,3,6,13,26,48,75,98,107,98,75,48,26,13,6,3,1,2,5,11,25,46,72,95,104,95,72,46,25,11,5,2,1,11,24,58,124,229,357,466,509,466,357,229,124,58,24,11,21,54,119,223,349,457,500,457,349,223,119,54,21,19,49,109,202,317,414,453,414,317,202,109,49,19,2,3,6,13,27,50,78,101,110,101,78,50,27,13,6,3,2,1,2,4,10,22,41,64,84,92,84,64,41,22,10,4,2,1,4,5,7,13,25,44,67,87,95,87,67,44,25,13,7,5,4,6,8,15,28,48,73,94,102,94,73,48,28,15,8,6,10,23,42,66,86,94,86,66,42,23,10,5,11,23,42,65,85,93,85,65,42,23,11,5,4,6,12,25,44,68,88,96,88,68,44,25,12,6,4,7,13,27,48,75,97,106,97,75,48,27,13,7,3,6,13,27,50,77,101,110,101,77,50,27,13,6,3,58,129,241,377,494,540,494,377,241,129,58,5,12,26,48,75,99,108,99,75,48,26,12,5,5,12,25,45,70,92,100,92,70,45,25,12,5,5,6,8,15,28,49,74,96,104,96,74,49,28,15,8,6,5,59,129,241,376,492,538,492,376,241,129,59,1,2,4,11,24,44,69,91,99,91,69,44,24,11,4,2,1,6,8,14,27,46,69,90,98,90,69,46,27,14,8,6,16,29,51,78,100,109,100,78,51,29,16,5,10,24,58,126,233,363,475,519,475,363,233,126,58,24,10,5,58,129,243,380,498,545,498,380,243,129,58,12,24,45,69,90,98,90,69,45,24,12,8,15,28,48,73,94,102,94,73,48,28,15,8,2,5,12,25,47,73,96,105,96,73,47,25,12,5,2,15,29,51,78,101,110,101,78,51,29,15,8,15,29,51,78,102,111,102,78,51,29,15,8,11,24,44,67,88,96,88,67,44,24,11,10,23,42,66,86,94,86,66,42,23,10,5,6,8,15,28,48,73,94,103,94,73,48,28,15,8,6,5,8,14,27,46,70,90,98,90,70,46,27,14,8,25,60,129,239,372,486,532,486,372,239,129,60,25,9,21,51,110,204,319,416,455,416,319,204,110,51,21,9,56,119,220,343,448,489,448,343,220,119,56,3,4,7,14,28,50,78,101,110,101,78,50,28,14,7,4,3,14,28,51,79,103,112,103,79,51,28,14],
"C" : [53,114,212,330,431,472,431,330,212,114,53,20,52,115,215,336,440,481,440,336,215,115,52,20,19,49,110,206,323,423,463,423,323,206,110,49,19,2,6,12,23,35,46,51,46,35,23,12,6,2,8,14,25,37,48,52,48,37,25,14,8,5,7,10,17,28,42,53,58,53,42,28,17,10,7,5,8,14,25,38,49,53,49,38,25,14,8,1,1,2,5,11,21,32,42,46,42,32,21,11,5,2,1,1,8,14,25,37,48,52,48,37,25,14,8,5,9,22,52,113,209,326,426,465,426,326,209,113,52,22,9,5,6,12,22,33,43,47,43,33,22,12,6,4,7,13,23,35,44,48,44,35,23,13,7,4,6,9,16,27,40,52,56,52,40,27,16,9,6,50,110,204,319,417,455,417,319,204,110,50,3,5,8,15,26,40,51,56,51,40,26,15,8,5,3,3,4,8,14,24,37,48,52,48,37,24,14,8,4,3,2,2,3,6,12,22,33,43,47,43,33,22,12,6,3,2,2,3,4,8,14,25,38,49,53,49,38,25,14,8,4,3,8,14,24,35,45,49,45,35,24,14,8,7,21,53,118,221,345,452,494,452,345,221,118,53,21,7,19,49,110,205,322,421,461,421,322,205,110,49,19,57,127,238,373,489,535,489,373,238,127,57,1,1,3,6,13,24,38,49,54,49,38,24,13,6,3,1,1,4,4,6,9,16,27,40,51,56,51,40,27,16,9,6,4,4,3,5,8,15,26,40,51,56,51,40,26,15,8,5,3,6,13,24,38,50,54,50,38,24,13,6,3,6,13,24,37,48,53,48,37,24,13,6,3,2,4,7,14,25,38,50,54,50,38,25,14,7,4,2,7,13,23,36,46,50,46,36,23,13,7,6,11,26,62,134,248,387,505,553,505,387,248,134,62,26,11,6,2,6,12,22,34,45,49,45,34,22,12,6,2,6,12,23,35,46,50,46,35,23,12,6,4,5,9,15,26,38,49,54,49,38,26,15,9,5,4,3,8,22,58,128,239,374,489,535,489,374,239,128,58,22,8,3,2,3,7,14,24,37,48,52,48,37,24,14,7,3,2,1,1,3,6,13,24,38,49,54,49,38,24,13,6,3,1,1,5,7,10,17,28,41,53,57,53,41,28,17,10,7,5,3,7,13,24,37,48,52,48,37,24,13,7,3,3,6,12,22,33,43,47,43,33,22,12,6,3,3,7,21,53,118,221,345,452,494,452,345,221,118,53,21,7,3,2,6,18,49,109,204,320,419,458,419,320,204,109,49,18,6,2,5,9,21,52,111,206,321,420,459,420,321,206,111,52,21,9,5,5,7,10,17,28,41,52,57,52,41,28,17,10,7,5,6,13,25,38,50,55,50,38,25,13,6,3,6,12,22,34,44,48,44,34,22,12,6,3,3,5,8,15,25,38,50,54,50,38,25,15,8,5,3,4,8,14,25,37,48,52,48,37,25,14,8,4,2,4,7,14,24,37,48,53,48,37,24,14,7,4,2,6,12,22,33,43,47,43,33,22,12,6,22,57,128,240,376,492,538,492,376,240,128,57,22,3,6,12,22,33,43,47,43,33,22,12,6,3,5,5,6,9,15,25,36,46,50,46,36,25,15,9,6,5,5,8,14,24,36,47,51,47,36,24,14,8,2,6,20,52,116,217,341,446,488,446,341,217,116,52,20,6,2,5,6,10,16,26,39,49,53,49,39,26,16,10,6,5,9,15,25,37,47,51,47,37,25,15,9,4,4,5,9,15,25,38,49,53,49,38,25,15,9,5,4,4,6,12,22,34,45,49,45,34,22,12,6,54,119,221,346,453,496,453,346,221,119,54,25,61,131,242,376,492,538,492,376,242,131,61,25,7,21,55,123,230,361,473,517,473,361,230,123,55,21,7,9,16,27,41,52,57,52,41,27,16,9,5,8,14,24,35,45,49,45,35,24,14,8,5,7,13,24,36,47,51,47,36,24,13,7,6,12,23,35,46,50,46,35,23,12,6,5,5,6,10,16,27,39,50,54,50,39,27,16,10,6,5,5,6,10,16,26,39,49,53,49,39,26,16,10,6,6,9,15,25,37,46,50,46,37,25,15,9,6,4,5,9,15,25,37,47,51,47,37,25,15,9,5,4,10,16,27,40,50,55,50,40,27,16,10,4,9,23,58,128,238,371,485,531,485,371,238,128,58,23,9,4,58,128,237,371,485,530,485,371,237,128,58],
"G" : [6,9,14,21,26,28,26,21,14,9,6,2,4,7,12,18,23,25,23,18,12,7,4,2,2,3,7,13,20,26,28,26,20,13,7,3,2,20,53,119,222,349,457,499,457,349,222,119,53,20,58,126,235,367,480,525,480,367,235,126,58,5,6,7,11,16,23,28,30,28,23,16,11,7,6,5,5,8,13,20,25,27,25,20,13,8,5,1,1,2,3,7,12,18,24,26,24,18,12,7,3,2,1,1,5,8,14,20,25,27,25,20,14,8,5,4,4,5,6,10,15,22,27,29,27,22,15,10,6,5,4,4,51,113,211,331,433,473,433,331,211,113,51,3,5,8,14,20,25,27,25,20,14,8,5,3,4,6,9,14,20,25,27,25,20,14,9,6,4,5,8,13,20,25,27,25,20,13,8,5,9,22,56,123,228,356,466,510,466,356,228,123,56,22,9,3,4,5,9,14,21,27,29,27,21,14,9,5,4,3,2,2,2,4,7,12,19,24,26,24,19,12,7,4,2,2,2,3,4,5,9,14,21,27,29,27,21,14,9,5,4,3,6,10,15,22,27,29,27,22,15,10,6,2,2,4,7,12,18,23,25,23,18,12,7,4,2,2,2,3,7,12,19,24,26,24,19,12,7,3,2,3,7,13,20,25,28,25,20,13,7,3,2,7,20,53,119,223,350,459,502,459,350,223,119,53,20,7,2,5,9,21,51,111,205,319,417,456,417,319,205,111,51,21,9,5,8,21,53,116,215,336,439,480,439,336,215,116,53,21,8,3,6,11,17,23,25,23,17,11,6,3,2,3,7,12,18,24,26,24,18,12,7,3,2,2,2,4,7,13,19,25,27,25,19,13,7,4,2,2,4,7,12,19,24,26,24,19,12,7,4,5,5,6,7,11,17,24,30,32,30,24,17,11,7,6,5,5,21,56,124,233,365,478,523,478,365,233,124,56,21,3,7,12,19,24,26,24,19,12,7,3,4,4,6,9,14,20,25,27,25,20,14,9,6,4,4,2,2,2,4,7,13,19,24,27,24,19,13,7,4,2,2,2,7,19,50,110,205,321,420,459,420,321,205,110,50,19,7,1,1,1,3,6,11,18,23,25,23,18,11,6,3,1,1,1,5,6,7,11,16,23,28,30,28,23,16,11,7,6,5,2,4,7,12,19,24,26,24,19,12,7,4,2,3,4,8,14,21,27,29,27,21,14,8,4,3,2,2,2,4,7,13,19,24,26,24,19,13,7,4,2,2,2,1,1,2,3,7,13,19,25,28,25,19,13,7,3,2,1,1,4,4,5,6,10,15,21,27,29,27,21,15,10,6,5,4,4,10,22,52,112,206,321,419,458,419,321,206,112,52,22,10,57,127,238,373,488,534,488,373,238,127,57,20,51,112,209,327,428,468,428,327,209,112,51,20,3,4,5,9,14,21,26,28,26,21,14,9,5,4,3,3,5,8,13,19,25,27,25,19,13,8,5,3,2,2,4,7,12,19,24,26,24,19,12,7,4,2,2,4,8,13,20,25,28,25,20,13,8,4,2,3,7,12,18,24,26,24,18,12,7,3,2,21,54,119,222,347,454,496,454,347,222,119,54,21,5,5,5,7,10,15,22,27,29,27,22,15,10,7,5,5,5,5,9,15,21,27,30,27,21,15,9,5,1,1,2,3,7,12,18,24,26,24,18,12,7,3,2,1,1,11,24,57,123,227,354,463,506,463,354,227,123,57,24,11,7,10,16,22,27,30,27,22,16,10,7,4,4,4,6,9,15,21,26,29,26,21,15,9,6,4,4,4,3,7,12,19,24,26,24,19,12,7,3,4,7,12,17,22,24,22,17,12,7,4,6,7,11,17,23,29,32,29,23,17,11,7,6,1,2,3,7,12,19,25,27,25,19,12,7,3,2,1,55,120,222,346,452,494,452,346,222,120,55,23,57,123,229,357,466,510,466,357,229,123,57,23,53,118,220,344,450,492,450,344,220,118,53,3,6,12,18,24,26,24,18,12,6,3,5,5,5,7,11,16,22,28,30,28,22,16,11,7,5,5,5,5,7,10,16,22,27,30,27,22,16,10,7,5,6,7,11,17,24,30,32,30,24,17,11,7,6,4,4,6,9,14,19,24,26,24,19,14,9,6,4,4,7,10,15,22,27,29,27,22,15,10,7,3,3,3,5,9,14,20,26,28,26,20,14,9,5,3,3,3,5,8,14,20,25,28,25,20,14,8,5],
"T" : [5,6,8,11,13,14,13,11,8,6,5,2,2,4,6,8,10,11,10,8,6,4,2,2,1,2,3,5,8,10,11,10,8,5,3,2,1,1,1,3,5,7,9,10,9,7,5,3,1,1,4,5,7,10,12,13,12,10,7,5,4,10,24,56,121,223,347,453,495,453,347,223,121,56,24,10,51,112,208,324,424,463,424,324,208,112,51,2,6,19,49,109,205,321,421,460,421,321,205,109,49,19,6,2,4,5,7,9,11,12,11,9,7,5,4,4,4,4,4,6,8,10,12,13,12,10,8,6,4,4,4,4,3,4,6,9,11,12,11,9,6,4,3,22,56,122,227,355,464,508,464,355,227,122,56,22,4,5,6,8,11,13,14,13,11,8,6,5,4,4,5,7,9,11,12,11,9,7,5,4,3,3,4,5,7,10,12,13,12,10,7,5,4,3,3,8,21,52,113,210,328,429,469,429,328,210,113,52,21,8,2,2,2,3,4,6,8,10,11,10,8,6,4,3,2,2,2,3,3,4,5,7,10,12,13,12,10,7,5,4,3,3,5,6,8,11,13,14,13,11,8,6,5,2,2,3,4,6,9,11,12,11,9,6,4,3,2,2,1,1,3,5,7,9,10,9,7,5,3,1,1,1,3,5,7,9,10,9,7,5,3,1,1,1,1,2,3,5,8,10,11,10,8,5,3,2,1,1,1,4,4,4,4,6,8,10,12,13,12,10,8,6,4,4,4,4,3,3,4,5,7,10,12,13,12,10,7,5,4,3,3,48,108,202,316,414,453,414,316,202,108,48,20,52,116,218,341,446,488,446,341,218,116,52,20,7,20,51,112,209,327,428,468,428,327,209,112,51,20,7,3,4,6,9,12,12,12,9,6,4,3,5,5,5,6,7,9,12,14,15,14,12,9,7,6,5,5,5,1,2,3,5,8,10,11,10,8,5,3,2,1,56,126,237,371,486,531,486,371,237,126,56,4,4,5,6,8,11,13,14,13,11,8,6,5,4,4,2,2,2,2,4,6,8,10,11,10,8,6,4,2,2,2,2,2,2,3,4,6,9,11,12,11,9,6,4,3,2,2,2,6,19,49,110,205,322,422,461,422,322,205,110,49,19,6,2,5,5,6,7,9,12,14,15,14,12,9,7,6,5,5,2,3,4,6,8,10,11,10,8,6,4,3,2,2,2,4,6,8,10,11,10,8,6,4,2,2,2,2,2,3,4,6,9,11,12,11,9,6,4,3,2,2,2,1,1,1,1,3,5,7,9,10,9,7,5,3,1,1,1,1,4,4,4,5,6,8,11,13,14,13,11,8,6,5,4,4,4,5,5,6,7,9,12,14,15,14,12,9,7,6,5,5,2,3,5,8,10,11,10,8,5,3,2,2,3,4,6,9,11,12,11,9,6,4,3,2,9,22,55,120,223,348,455,497,455,348,223,120,55,22,9,23,57,126,234,365,477,522,477,365,234,126,57,23,8,22,58,128,239,374,490,536,490,374,239,128,58,22,8,3,4,6,9,11,12,11,9,6,4,3,1,2,3,5,8,10,11,10,8,5,3,2,1,2,3,4,6,9,11,12,11,9,6,4,3,2,6,10,22,52,111,205,320,417,456,417,320,205,111,52,22,10,6,4,5,7,9,12,12,12,9,7,5,4,1,1,1,1,3,5,7,9,10,9,7,5,3,1,1,1,1,5,5,6,7,9,12,14,15,14,12,9,7,6,5,5,54,117,215,335,437,478,437,335,215,117,54,4,4,4,4,6,8,10,12,13,12,10,8,6,4,4,4,4,2,3,5,8,11,11,11,8,5,3,2,3,4,6,9,11,12,11,9,6,4,3,5,5,7,9,11,13,14,13,11,9,7,5,5,1,1,2,3,5,7,10,10,10,7,5,3,2,1,1,5,6,8,11,13,14,13,11,8,6,5,4,4,6,8,10,12,13,12,10,8,6,4,4,3,4,6,9,11,12,11,9,6,4,3,55,123,231,363,475,520,475,363,231,123,55,6,10,24,56,121,223,347,453,495,453,347,223,121,56,24,10,6,23,54,115,213,331,432,472,432,331,213,115,54,23,5,6,7,9,11,14,14,14,11,9,7,6,5,4,4,5,6,8,10,12,13,12,10,8,6,5,4,4,6,7,9,12,14,15,14,12,9,7,6,3,3,3,4,5,7,10,12,13,12,10,7,5,4,3,3,3,4,5,7,10,12,13,12,10,7,5,4],
"peak" : [5,17,30,43,55,68,81,95,109,123,137,149,162,174,187,202,218,234,247,260,274,286,300,317,333,346,358,372,385,399,414,426,439,455,471,487,503,517,530,545,562,579,595,608,620,634,648,662,675,687,700,715,729,743,759,772,786,800,811,823,837,850,862,874,885,899,914,927,941,954,968,982]
}
}
],
"highlight" : [{"color" : "rgb(120,120,180)","offset" : 80,"width" : 1},{"color" : "rgb(180,20,180)","offset" : 185,"width" : 1}],
"name" : "Sanger Sequencing (Multiple sequeneces)",
"subtype" : "DNA",
"type" : "sequence"
},
{
"autowidth" : true,
"data" : [{"data" : [7,5,5,5,6,7,9,8,8,8,8,5,7,9,15,15,16,9,9,7,8,10,9,21,22,22,24,20,24,26,24,25,24,31,29,33,33,33,33,33,20,17,19,18,18,18,27,23,31,26,31,31,31,34,32,31,30,30,30,30,30,24,24,20,21,17,17,27,29,25,31,31,31],
"id" : "R1-0000-5678-SQ",
"offset" : 126
}
],
"height" : 10,
"name" : "Sequence Quality",
"type" : "heatmap"
},
{
"data" : [{"data" : [{"fill" : "green","side" : "left","title" : "Rate Line 123","type" : "line","xAxis" : "offset","yAxis" : "rate"},{"fill" : "blue","side" : "left","title" : "Rate Line 234","type" : "line","xAxis" : "offset","yAxis" : "rate2"},{"fill" : "red","side" : "right","title" : "Rate Line Ref","type" : "scatter","xAxis" : "offset","yAxis" : "rate3"}],
"id" : "Data-frame",
"offset" : 10
}
],
"dataframe" : {
"offset" : [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,51,52,53,54,55,56,57,58,59,60,61,62,63,64,65,66,67,68,69,70,71,72,73,74,75,76,77,78,79,80,81,82,83,84,85,86,87,88,89,90,91,92,93,94,95,96,97,98,99,100,101,102,103,104,105,106,107,108,109,110,111,112,113,114,115,116,117,118,119,120,121,122,123,124,125,126,127,128,129,130,131,132,133,134,135,136,137,138,139,140,141,142,143,144,145,146,147,148,149,150,151,152,153,154,155,156,157,158,159,160,161,162,163,164,165,166,167,168,169,170,171,172,173,174,175,176,177,178,179,180,181,182,183,184,185,186,187,188,189,190,191,192,193,194,195,196,197,198,199,200,201,202,203,204,205,206,207,208,209,210,211,212,213,214,215,216,217,218,219,220,221,222,223,224,225,226,227,228,229,230,231,232,233,234,235,236,237,238,239,240,241,242,243,244,245,246,247,248,249,250,251,252,253,254,255,256,257,258,259,260,261,262,263,264,265,266,267,268,269,270,271,272,273,274,275,276,277,278,279,280,281,282,283,284,285,286,287,288,289,290,291,292,293,294,295,296,297,298,299,300,301,302,303,304,305,306,307,308,309,310,311,312,313,314,315,316,317,318,319,320,321,322,323,324,325,326,327,328,329,330,331,332,333,334,335,336,337,338,339,340,341,342,343,344,345,346,347,348,349,350,351,352,353,354,355,356,357,358,359,360,361,362,363,364,365,366,367,368,369,370,371,372,373,374,375,376,377,378,379,380,381,382,383,384,385,386,387,388,389,390,391,392,393,394,395,396,397,398,399,400,401,402,403,404,405,406,407,408,409],
"rate" : [53,114,212,330,431,472,431,330,212,114,53,20,52,115,215,336,440,481,440,336,215,115,52,20,19,49,110,206,323,423,463,423,323,206,110,49,19,2,6,12,23,35,46,51,46,35,23,12,6,2,8,14,25,37,48,52,48,37,25,14,8,5,7,10,17,28,42,53,58,53,42,28,17,10,7,5,8,14,25,38,49,53,49,38,25,14,8,1,1,2,5,11,21,32,42,46,42,32,21,11,5,2,1,1,8,14,25,37,48,52,48,37,25,14,8,5,9,22,52,113,209,326,426,465,426,326,209,113,52,22,9,5,6,12,22,33,43,47,43,33,22,12,6,4,7,13,23,35,44,48,44,35,23,13,7,4,6,9,16,27,40,52,56,52,40,27,16,9,6,50,110,204,319,417,455,417,319,204,110,50,3,5,8,15,26,40,51,56,51,40,26,15,8,5,3,3,4,8,14,24,37,48,52,48,37,24,14,8,4,3,2,2,3,6,12,22,33,43,47,43,33,22,12,6,3,2,2,3,4,8,14,25,38,49,53,49,38,25,14,8,4,3,8,14,24,35,45,49,45,35,24,14,8,7,21,53,118,221,345,452,494,452,345,221,118,53,21,7,19,49,110,205,322,421,461,421,322,205,110,49,19,57,127,238,373,489,535,489,373,238,127,57,1,1,3,6,13,24,38,49,54,49,38,24,13,6,3,1,1,4,4,6,9,16,27,40,51,56,51,40,27,16,9,6,4,4,3,5,8,15,26,40,51,56,51,40,26,15,8,5,3,6,13,24,38,50,54,50,38,24,13,6,3,6,13,24,37,48,53,48,37,24,13,6,3,2,4,7,14,25,38,50,54,50,38,25,14,7,4,2,7,13,23,36,46,50,46,36,23,13,7,6,11,26,62,134,248,387,505,553],
"rate2" : [2,4,7,14,26,39,51,56,51,39,26,14,7,4,2,3,3,5,8,15,27,41,52,57,52,41,27,15,8,5,3,3,3,5,8,15,26,39,51,55,51,39,26,15,8,5,3,2,5,11,21,33,43,47,43,33,21,11,5,2,51,112,209,326,427,467,427,326,209,112,51,2,7,22,57,129,241,378,495,541,495,378,241,129,57,22,7,2,22,58,129,242,380,497,544,497,380,242,129,58,22,6,12,22,34,44,48,44,34,22,12,6,1,2,6,12,23,35,46,50,46,35,23,12,6,2,1,10,17,28,42,53,58,53,42,28,17,10,9,15,25,36,46,50,46,36,25,15,9,1,1,3,6,13,23,36,48,52,48,36,23,13,6,3,1,1,10,16,26,38,48,52,48,38,26,16,10,1,1,3,6,13,24,38,50,54,50,38,24,13,6,3,1,1,54,121,226,355,464,508,464,355,226,121,54,5,8,15,27,41,53,57,53,41,27,15,8,5,3,4,8,14,24,36,46,50,46,36,24,14,8,4,3,2,5,12,21,33,44,48,44,33,21,12,5,2,23,57,124,230,358,468,512,468,358,230,124,57,23,5,9,15,25,38,48,52,48,38,25,15,9,5,7,13,23,35,45,49,45,35,23,13,7,1,2,6,12,22,34,45,49,45,34,22,12,6,2,1,8,15,26,40,52,56,52,40,26,15,8,7,15,26,40,52,56,52,40,26,15,7,9,22,53,116,214,334,436,477,436,334,214,116,53,22,9,53,114,210,327,427,467,427,327,210,114,53,2,7,21,57,127,238,373,488,534,488,373,238,127,57,8,4,3,8,14,24,35,45,49,45,35,24,14,8,7,21,53,118,221,345,452,494,452,345,221,118,53,21,7,19,49,110,205,322,421,461,421,322,205,110],
"rate3" : [3,3,5,8,15,26,40,51,56,51,40,26,15,8,5,3,3,22,57,126,234,367,480,525,480,367,234,126,57,22,6,12,22,33,43,47,43,33,22,12,6,3,3,4,8,14,24,36,46,50,46,36,24,14,8,4,3,3,7,13,23,34,44,48,44,34,23,13,7,52,112,206,321,419,458,419,321,206,112,52,3,4,8,14,24,37,47,52,47,37,24,14,8,4,3,3,7,14,24,37,48,52,48,37,24,14,7,3,10,17,29,42,54,58,54,42,29,17,10,3,7,13,23,35,45,49,45,35,23,13,7,3,4,4,5,9,16,26,39,50,54,50,39,26,16,9,5,4,4,4,7,14,25,38,49,53,49,38,25,14,7,4,7,14,25,39,51,55,51,39,25,14,7,7,10,17,27,41,52,56,52,41,27,17,10,7,6,19,50,112,210,329,430,471,430,329,210,112,50,19,6,2,6,18,49,109,204,320,419,459,419,320,204,109,49,18,6,2,55,121,224,351,458,501,458,351,224,121,55,5,9,15,25,37,48,52,48,37,25,15,9,5,2,3,7,13,23,36,47,51,47,36,23,13,7,3,2,4,7,13,23,34,44,48,44,34,23,13,7,4,3,5,8,15,27,41,53,57,53,41,27,15,8,5,3,1,2,6,12,23,35,46,50,46,35,23,12,6,2,1,6,12,23,35,46,50,46,35,23,12,6,4,8,14,24,37,47,51,47,37,24,14,8,4,2,7,21,55,124,232,363,475,520,475,363,232,124,55,21,7,2,4,7,14,25,38,50,54,50,38,25,14,7,4,1,2,6,12,23,35,46,51,46,35,23,12,6,2,1,7,13,23,35,45,49,45,35,23,13,7,2,7,22,57,113,209,326,426,465,426,326,209,113,52,22,9,5,6,12,22]
},
"height" : 100,
"name" : "Recombination Rates",
"type" : "dataframe"
},
{
"data" : [{"data" : [[10,16,17,18,19,21,44,46,47,50,51,57,58,59,62,64,67,68,69,82,83,88,89,90,91,96,97,98,108,109,112,114,118,119,120,124,125,126,127,132,133,134,141,150,154,158,167,173,175,182,183,188,347,349,351,354,356,359,360,365,366,374,377,378,379,382,383,384,387,388,389,390,391]
],
"fill" : ["blue"]
}
],
"id" : "protein_altering",
"name" : "Protein Altering",
"type" : "marker"
},
{
"data" : [{"data" : [[121,196]
],
"dir" : "left",
"fill" : "rgb(255,255,51)",
"id" : "clone-1234567",
"outline" : "rgb(0,0,0)"
},
{
"data" : [[371,400]
],
"dir" : "right",
"fill" : "rgb(255,255,51)",
"id" : "clone-2345678",
"landmarks" : [{"offset" : 157,"text" : "Gap "},{"offset" : 137,"text" : "Insertion "}],
"outline" : "rgb(0,0,0)"
}
],
"name" : "Clones",
"type" : "box"
},
{
"data" : [{"fill" : "rgb(100,0,0)","id" : "SNP123","offset" : 23,"outline" : "rgb(0,0,0)"},{"fill" : "rgb(100,0,0)","id" : "SNP234","offset" : 45,"outline" : "rgb(0,0,0)"},{"fill" : "rgb(100,0,0)","id" : "SNP345","offset" : 135,"outline" : "rgb(0,0,0)"},{"fill" : "rgb(100,0,0)","id" : "SNP456","offset" : 172,"outline" : "rgb(0,0,0)"},{"fill" : "rgb(100,0,0)","id" : "SNP567","offset" : 180,"outline" : "rgb(0,0,0)"},{"fill" : "rgb(100,0,0)","id" : "SNP678","offset" : 190,"outline" : "rgb(0,0,0)"},{"fill" : "rgb(100,0,0)","id" : "SNP789","offset" : 195,"outline" : "rgb(0,0,0)"}],
"name" : "SNP Location",
"type" : "triangle"
},
{
"data" : [{"id" : "SNP123","offset" : 19,"sequence" : "CACA[AT]GCACCTTGTA"
},
{
"id" : "SNP234",
"offset" : 41,
"sequence" : "ATCG[TG]AATA"
},
{
"id" : "SNP789",
"offset" : 116,
"sequence" : "GCCC[CT]AGGG"
}
],
"name" : "SNP Sequences",
"subtype" : "DNA",
"type" : "sequence"
}
]
}
// Create the configuration for the graph
var config = {
"background" : "rgb(245,245,245)",
"dataPointSize" : 5,
"featureStaggered" : true,
"graphType" : "Genome"
}
// Event used to create graph (optional)
var events = false
// Call the CanvasXpress function to create the graph
var cX = new CanvasXpress("canvasId", data, config, events);
</script>
</body>
</html>
library(canvasXpress)
library(jsonlite)
genome <- read_json("https://www.canvasxpress.org/data/r/cX-genomeadvanced.json")
canvasXpress(
data=genome,
background="rgb(245,245,245)",
dataPointSize=5,
featureStaggered=TRUE,
graphType="Genome"
)
from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import show_in_browser
if __name__ == "__main__":
# Define the chart with its data and configuration
chart: CanvasXpress = CanvasXpress(
render_to = "genome3",
data = {
"tracks": [
{
"connect": True,
"data": [
{
"data": [
[10, 20],
[30, 40],
[50, 60],
[70, 80],
[90, 100],
[110, 120]
],
"dir": "right",
"fill": "rgb(255,255,51)",
"id": "123456_at",
"outline": "rgb(0,0,0)",
"sequences": ["GTTTTACGTAC", "TACGTACGTAC", "GGTTTACGTAC", "GGTTTACGTAC", "GGTTTACGTAC", "GGTTTACGTAC"]
},
{
"data": [
[50, 60],
[70, 80],
[90, 100],
[110, 120],
[130, 140],
[150, 160]
],
"dir": "left",
"fill": "rgb(255,255,51)",
"id": "234567_at",
"outline": "rgb(0,0,0)"
},
{
"data": [
[100, 110],
[120, 130],
[140, 150],
[160, 170],
[180, 190]
],
"dir": "right",
"fill": "rgb(255,255,51)",
"id": "345678_at",
"outline": "rgb(0,0,0)"
}
],
"name": "Affymetrix Probes",
"type": "box"
},
{
"data": [
{
"data": [25, 35, 46],
"id": "123456_at",
"offset": 10
},
{
"data": [80, 45, 10],
"id": "234567_at",
"offset": 50
},
{
"data": [65, 46, 29],
"id": "345678_at",
"offset": 100
}
],
"height": 20,
"name": "Heatmap for Tissue Distribution for Heart (top), Liver (middle), Kidney (bottom)",
"type": "heatmap"
},
{
"data": [
{
"data": [25, 35, 46],
"id": "123456_at",
"offset": 10
},
{
"data": [80, 45, 10],
"id": "234567_at",
"offset": 50
},
{
"data": [65, 46, 29],
"id": "345678_at",
"offset": 100
}
],
"fill": ["rgb(255,0,0)", "rgb(0,0,255)", "rgb(255,255,0)"],
"height": 50,
"name": "Bar graph Tissue Distribution for Heart, Liver and Kidney",
"outline": ["rgb(255,0,0)", "rgb(0,0,255)", "rgb(255,255,0)"],
"type": "bar"
},
{
"data": [
{
"dir": "right",
"fill": "rgb(51,255,255)",
"id": "Reference",
"offset": 1,
"outline": "rgb(0,0,0)",
"sequence": "AAAACCCGGGTTTTACGTACGTACGTACGTACGTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTAAACC",
"translate": [-3, -2, -1, 1, 2, 3]
},
{
"coordinate": 50,
"dir": "right",
"fill": "rgb(255,255,51)",
"gaps": [
[18, 1],
[22, 1]
],
"id": "R1-0000-1234",
"offset": 1,
"outline": "rgb(0,0,0)",
"sequence": "AAAACCCGGGTTTTACGTCGTAGTACGTACGTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAA",
"trace": {
"A": [57, 127, 237, 371, 486, 531, 486, 371, 237, 127, 57, 54, 117, 217, 339, 442, 484, 442, 339, 217, 117, 54, 10, 24, 60, 130, 240, 375, 490, 535, 490, 375, 240, 130, 60, 24, 10, 56, 121, 222, 346, 452, 494, 452, 346, 222, 121, 56, 7, 14, 27, 48, 74, 95, 104, 95, 74, 48, 27, 14, 7, 6, 8, 14, 27, 46, 69, 90, 98, 90, 69, 46, 27, 14, 8, 6, 4, 5, 7, 14, 27, 47, 72, 93, 101, 93, 72, 47, 27, 14, 7, 5, 4, 5, 11, 23, 42, 65, 85, 92, 85, 65, 42, 23, 11, 5, 7, 14, 27, 48, 74, 95, 104, 95, 74, 48, 27, 14, 7, 1, 2, 4, 10, 22, 42, 65, 85, 93, 85, 65, 42, 22, 10, 4, 2, 1, 5, 12, 24, 44, 68, 88, 97, 88, 68, 44, 24, 12, 5, 4, 5, 7, 14, 27, 47, 72, 94, 102, 94, 72, 47, 27, 14, 7, 5, 4, 2, 4, 10, 22, 41, 64, 83, 91, 83, 64, 41, 22, 10, 4, 2, 12, 24, 43, 67, 87, 95, 87, 67, 43, 24, 12, 21, 52, 113, 210, 328, 429, 469, 429, 328, 210, 113, 52, 21, 4, 6, 13, 26, 47, 72, 93, 102, 93, 72, 47, 26, 13, 6, 4, 4, 6, 13, 26, 46, 71, 92, 100, 92, 71, 46, 26, 13, 6, 4, 6, 8, 14, 27, 46, 69, 89, 97, 89, 69, 46, 27, 14, 8, 6, 4, 5, 8, 14, 28, 49, 76, 98, 107, 98, 76, 49, 28, 14, 8, 5, 4, 7, 13, 25, 45, 68, 88, 96, 88, 68, 45, 25, 13, 7, 5, 11, 24, 43, 67, 88, 96, 88, 67, 43, 24, 11, 5, 22, 54, 118, 219, 342, 447, 489, 447, 342, 219, 118, 54, 22, 5, 12, 25, 46, 71, 93, 102, 93, 71, 46, 25, 12, 5, 5, 12, 24, 44, 68, 89, 97, 89, 68, 44, 24, 12, 5, 20, 54, 121, 226, 355, 465, 508, 465, 355, 226, 121, 54, 20, 3, 4, 6, 13, 25, 45, 70, 91, 99, 91, 70, 45, 25, 13, 6, 4, 3, 6, 8, 15, 27, 47, 71, 91, 99, 91, 71, 47, 27, 15, 8, 6, 1, 2, 4, 11, 24, 44, 69, 90, 98, 90, 69, 44, 24, 11, 4, 2, 1, 6, 11, 25, 60, 128, 237, 369, 482, 527, 482, 369, 237, 128, 60, 25, 11, 6, 2, 5, 12, 25, 47, 74, 97, 106, 97, 74, 47, 25, 12, 5, 2, 5, 8, 15, 29, 51, 78, 101, 110, 101, 78, 51, 29, 15, 8, 5, 5, 12, 26, 48, 75, 98, 107, 98, 75, 48, 26, 12, 5, 6, 18, 48, 107, 201, 315, 412, 451, 412, 315, 201, 107, 48, 18, 6, 9, 16, 31, 53, 81, 105, 114, 105, 81, 53, 31, 16, 9, 6, 8, 15, 28, 48, 73, 94, 103, 94, 73, 48, 28, 15, 8, 6, 11, 23, 42, 65, 85, 92, 85, 65, 42, 23, 11, 19, 51, 113, 212, 332, 434, 475, 434, 332, 212, 113, 51, 19, 8, 15, 28, 49, 74, 95, 104, 95, 74, 49, 28, 15, 8, 12, 26, 49, 76, 99, 109, 99, 76, 49, 26, 12, 12, 24, 43, 67, 86, 94, 86, 67, 43, 24, 12, 22, 54, 118, 218, 341, 445, 487, 445, 341, 218, 118, 54, 22, 21, 52, 112, 208, 324, 423, 462, 423, 324, 208, 112, 52, 21, 10, 23, 54, 115, 212, 330, 430, 471, 430, 330, 212, 115, 54, 23, 10, 2, 3, 5, 12, 25, 45, 69, 91, 99, 91, 69, 45, 25, 12, 5, 3, 2, 2, 3, 5, 12, 24, 44, 68, 88, 97, 88, 68, 44, 24, 12, 5, 3, 2, 8, 15, 28, 50, 77, 100, 109, 100, 77, 50, 28, 15, 8, 12, 26, 48, 74, 96, 105, 96, 74, 48, 26, 12, 13, 27, 48, 74, 96, 105, 96, 74, 48, 27, 13, 13, 25, 45, 70, 91, 99, 91, 70, 45, 25, 13, 7, 14, 28, 49, 75, 97, 105, 97, 75, 49, 28, 14, 7, 2, 5, 12, 26, 48, 74, 97, 106, 97, 74, 48, 26, 12, 5, 2, 16, 30, 53, 80, 103, 113, 103, 80, 53, 30, 16, 25, 61, 133, 246, 384, 501, 548, 501, 384, 246, 133, 61, 25, 6, 13, 25, 45, 69, 90, 98, 90, 69, 45, 25, 13, 6, 5, 6, 9, 15, 29, 50, 77, 99, 108, 99, 77, 50, 29, 15, 9, 6, 5, 10, 23, 42, 65, 86, 94, 86, 65, 42, 23, 10, 9, 23, 55, 120, 223, 348, 454, 497, 454, 348, 223, 120, 55, 23, 9, 2, 4, 11, 23, 43, 67, 88, 96, 88, 67, 43, 23, 11, 4, 2, 2, 3, 6, 12, 26, 48, 74, 96, 105, 96, 74, 48, 26, 12, 6, 3, 2, 15, 28, 49, 74, 96, 104, 96, 74, 49, 28, 15, 22, 55, 120, 223, 348, 455, 498, 455, 348, 223, 120, 55, 22, 22, 53, 115, 213, 332, 434, 474, 434, 332, 213, 115, 53, 22, 7, 20, 53, 118, 221, 346, 454, 496, 454, 346, 221, 118, 53, 20, 7, 2, 3, 5, 11, 24, 44, 67, 88, 96, 88, 67, 44, 24, 11, 5, 3, 2, 15, 28, 50, 75, 97, 106, 97, 75, 50, 28, 15, 1, 2, 5, 12, 25, 47, 74, 96, 105, 96, 74, 47, 25, 12, 5, 2, 1, 6, 8, 15, 28, 49, 74, 96, 104, 96, 74, 49, 28, 15, 8, 6, 5, 12, 26, 47, 72, 94, 103, 94, 72, 47, 26, 12, 5, 8, 15, 27, 47, 71, 92, 100, 92, 71, 47, 27, 15, 8, 3, 5, 11, 23, 42, 65, 84, 92, 84, 65, 42, 23, 11, 5, 3, 5, 12, 25, 45, 70, 91, 100, 91, 70, 45, 25, 12, 5, 1, 2, 4, 10, 22, 41, 64, 84, 92, 84, 64, 41, 22, 10, 4, 2, 1, 7, 20, 51, 113, 212, 331, 433, 474, 433, 331, 212, 113, 51, 20, 7, 2, 3, 5, 12, 25, 46, 72, 94, 102, 94, 72, 46, 25, 12, 5, 3, 2, 2, 4, 11, 25, 46, 72, 94, 102, 94, 72, 46, 25, 11, 4, 2, 2, 3, 6, 12, 26, 48, 74, 97, 106, 97, 74, 48, 26, 12, 6, 3, 2, 10, 25, 61, 133, 247, 386, 504, 551, 504, 386, 247, 133, 61, 25, 10, 15, 27, 47, 71, 92, 100, 92, 71, 47, 27, 15, 5, 8, 15, 28, 50, 76, 99, 108, 99, 76, 50, 28, 15, 8, 5, 2, 3, 6, 13, 26, 48, 75, 98, 107, 98, 75, 48, 26, 13, 6, 3, 2, 8, 22, 57, 127, 238, 372, 487, 532, 487, 372, 238, 127, 57, 22, 8, 60, 129, 237, 370, 483, 528, 483, 370, 237, 129, 60],
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"fill": "rgb(255,51,255)",
"id": "R1-0000-3456",
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"sequence": "AAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAAC",
"trace": {
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{
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"gaps": [
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"id": "R1-0000-4567",
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"sequence": "TAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCGGGTTTACGTACGTAAACCG",
"trace": {
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"sequence": "CCCGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAACCCGGGTTTAAACC",
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"peak": [5, 17, 30, 43, 55, 68, 81, 95, 109, 123, 137, 149, 162, 174, 187, 202, 218, 234, 247, 260, 274, 286, 300, 317, 333, 346, 358, 372, 385, 399, 414, 426, 439, 455, 471, 487, 503, 517, 530, 545, 562, 579, 595, 608, 620, 634, 648, 662, 675, 687, 700, 715, 729, 743, 759, 772, 786, 800, 811, 823, 837, 850, 862, 874, 885, 899, 914, 927, 941, 954, 968, 982]
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"color": "rgb(120,120,180)",
"offset": 80,
"width": 1
},
{
"color": "rgb(180,20,180)",
"offset": 185,
"width": 1
}
],
"name": "Sanger Sequencing (Multiple sequeneces)",
"subtype": "DNA",
"type": "sequence"
},
{
"autowidth": True,
"data": [
{
"data": [7, 5, 5, 5, 6, 7, 9, 8, 8, 8, 8, 5, 7, 9, 15, 15, 16, 9, 9, 7, 8, 10, 9, 21, 22, 22, 24, 20, 24, 26, 24, 25, 24, 31, 29, 33, 33, 33, 33, 33, 20, 17, 19, 18, 18, 18, 27, 23, 31, 26, 31, 31, 31, 34, 32, 31, 30, 30, 30, 30, 30, 24, 24, 20, 21, 17, 17, 27, 29, 25, 31, 31, 31],
"id": "R1-0000-5678-SQ",
"offset": 126
}
],
"height": 10,
"name": "Sequence Quality",
"type": "heatmap"
},
{
"data": [
{
"data": [
{
"fill": "green",
"side": "left",
"title": "Rate Line 123",
"type": "line",
"xAxis": "offset",
"yAxis": "rate"
},
{
"fill": "blue",
"side": "left",
"title": "Rate Line 234",
"type": "line",
"xAxis": "offset",
"yAxis": "rate2"
},
{
"fill": "red",
"side": "right",
"title": "Rate Line Ref",
"type": "scatter",
"xAxis": "offset",
"yAxis": "rate3"
}
],
"id": "Data-frame",
"offset": 10
}
],
"dataframe": {
"offset": [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167, 168, 169, 170, 171, 172, 173, 174, 175, 176, 177, 178, 179, 180, 181, 182, 183, 184, 185, 186, 187, 188, 189, 190, 191, 192, 193, 194, 195, 196, 197, 198, 199, 200, 201, 202, 203, 204, 205, 206, 207, 208, 209, 210, 211, 212, 213, 214, 215, 216, 217, 218, 219, 220, 221, 222, 223, 224, 225, 226, 227, 228, 229, 230, 231, 232, 233, 234, 235, 236, 237, 238, 239, 240, 241, 242, 243, 244, 245, 246, 247, 248, 249, 250, 251, 252, 253, 254, 255, 256, 257, 258, 259, 260, 261, 262, 263, 264, 265, 266, 267, 268, 269, 270, 271, 272, 273, 274, 275, 276, 277, 278, 279, 280, 281, 282, 283, 284, 285, 286, 287, 288, 289, 290, 291, 292, 293, 294, 295, 296, 297, 298, 299, 300, 301, 302, 303, 304, 305, 306, 307, 308, 309, 310, 311, 312, 313, 314, 315, 316, 317, 318, 319, 320, 321, 322, 323, 324, 325, 326, 327, 328, 329, 330, 331, 332, 333, 334, 335, 336, 337, 338, 339, 340, 341, 342, 343, 344, 345, 346, 347, 348, 349, 350, 351, 352, 353, 354, 355, 356, 357, 358, 359, 360, 361, 362, 363, 364, 365, 366, 367, 368, 369, 370, 371, 372, 373, 374, 375, 376, 377, 378, 379, 380, 381, 382, 383, 384, 385, 386, 387, 388, 389, 390, 391, 392, 393, 394, 395, 396, 397, 398, 399, 400, 401, 402, 403, 404, 405, 406, 407, 408, 409],
"rate": [53, 114, 212, 330, 431, 472, 431, 330, 212, 114, 53, 20, 52, 115, 215, 336, 440, 481, 440, 336, 215, 115, 52, 20, 19, 49, 110, 206, 323, 423, 463, 423, 323, 206, 110, 49, 19, 2, 6, 12, 23, 35, 46, 51, 46, 35, 23, 12, 6, 2, 8, 14, 25, 37, 48, 52, 48, 37, 25, 14, 8, 5, 7, 10, 17, 28, 42, 53, 58, 53, 42, 28, 17, 10, 7, 5, 8, 14, 25, 38, 49, 53, 49, 38, 25, 14, 8, 1, 1, 2, 5, 11, 21, 32, 42, 46, 42, 32, 21, 11, 5, 2, 1, 1, 8, 14, 25, 37, 48, 52, 48, 37, 25, 14, 8, 5, 9, 22, 52, 113, 209, 326, 426, 465, 426, 326, 209, 113, 52, 22, 9, 5, 6, 12, 22, 33, 43, 47, 43, 33, 22, 12, 6, 4, 7, 13, 23, 35, 44, 48, 44, 35, 23, 13, 7, 4, 6, 9, 16, 27, 40, 52, 56, 52, 40, 27, 16, 9, 6, 50, 110, 204, 319, 417, 455, 417, 319, 204, 110, 50, 3, 5, 8, 15, 26, 40, 51, 56, 51, 40, 26, 15, 8, 5, 3, 3, 4, 8, 14, 24, 37, 48, 52, 48, 37, 24, 14, 8, 4, 3, 2, 2, 3, 6, 12, 22, 33, 43, 47, 43, 33, 22, 12, 6, 3, 2, 2, 3, 4, 8, 14, 25, 38, 49, 53, 49, 38, 25, 14, 8, 4, 3, 8, 14, 24, 35, 45, 49, 45, 35, 24, 14, 8, 7, 21, 53, 118, 221, 345, 452, 494, 452, 345, 221, 118, 53, 21, 7, 19, 49, 110, 205, 322, 421, 461, 421, 322, 205, 110, 49, 19, 57, 127, 238, 373, 489, 535, 489, 373, 238, 127, 57, 1, 1, 3, 6, 13, 24, 38, 49, 54, 49, 38, 24, 13, 6, 3, 1, 1, 4, 4, 6, 9, 16, 27, 40, 51, 56, 51, 40, 27, 16, 9, 6, 4, 4, 3, 5, 8, 15, 26, 40, 51, 56, 51, 40, 26, 15, 8, 5, 3, 6, 13, 24, 38, 50, 54, 50, 38, 24, 13, 6, 3, 6, 13, 24, 37, 48, 53, 48, 37, 24, 13, 6, 3, 2, 4, 7, 14, 25, 38, 50, 54, 50, 38, 25, 14, 7, 4, 2, 7, 13, 23, 36, 46, 50, 46, 36, 23, 13, 7, 6, 11, 26, 62, 134, 248, 387, 505, 553],
"rate2": [2, 4, 7, 14, 26, 39, 51, 56, 51, 39, 26, 14, 7, 4, 2, 3, 3, 5, 8, 15, 27, 41, 52, 57, 52, 41, 27, 15, 8, 5, 3, 3, 3, 5, 8, 15, 26, 39, 51, 55, 51, 39, 26, 15, 8, 5, 3, 2, 5, 11, 21, 33, 43, 47, 43, 33, 21, 11, 5, 2, 51, 112, 209, 326, 427, 467, 427, 326, 209, 112, 51, 2, 7, 22, 57, 129, 241, 378, 495, 541, 495, 378, 241, 129, 57, 22, 7, 2, 22, 58, 129, 242, 380, 497, 544, 497, 380, 242, 129, 58, 22, 6, 12, 22, 34, 44, 48, 44, 34, 22, 12, 6, 1, 2, 6, 12, 23, 35, 46, 50, 46, 35, 23, 12, 6, 2, 1, 10, 17, 28, 42, 53, 58, 53, 42, 28, 17, 10, 9, 15, 25, 36, 46, 50, 46, 36, 25, 15, 9, 1, 1, 3, 6, 13, 23, 36, 48, 52, 48, 36, 23, 13, 6, 3, 1, 1, 10, 16, 26, 38, 48, 52, 48, 38, 26, 16, 10, 1, 1, 3, 6, 13, 24, 38, 50, 54, 50, 38, 24, 13, 6, 3, 1, 1, 54, 121, 226, 355, 464, 508, 464, 355, 226, 121, 54, 5, 8, 15, 27, 41, 53, 57, 53, 41, 27, 15, 8, 5, 3, 4, 8, 14, 24, 36, 46, 50, 46, 36, 24, 14, 8, 4, 3, 2, 5, 12, 21, 33, 44, 48, 44, 33, 21, 12, 5, 2, 23, 57, 124, 230, 358, 468, 512, 468, 358, 230, 124, 57, 23, 5, 9, 15, 25, 38, 48, 52, 48, 38, 25, 15, 9, 5, 7, 13, 23, 35, 45, 49, 45, 35, 23, 13, 7, 1, 2, 6, 12, 22, 34, 45, 49, 45, 34, 22, 12, 6, 2, 1, 8, 15, 26, 40, 52, 56, 52, 40, 26, 15, 8, 7, 15, 26, 40, 52, 56, 52, 40, 26, 15, 7, 9, 22, 53, 116, 214, 334, 436, 477, 436, 334, 214, 116, 53, 22, 9, 53, 114, 210, 327, 427, 467, 427, 327, 210, 114, 53, 2, 7, 21, 57, 127, 238, 373, 488, 534, 488, 373, 238, 127, 57, 8, 4, 3, 8, 14, 24, 35, 45, 49, 45, 35, 24, 14, 8, 7, 21, 53, 118, 221, 345, 452, 494, 452, 345, 221, 118, 53, 21, 7, 19, 49, 110, 205, 322, 421, 461, 421, 322, 205, 110],
"rate3": [3, 3, 5, 8, 15, 26, 40, 51, 56, 51, 40, 26, 15, 8, 5, 3, 3, 22, 57, 126, 234, 367, 480, 525, 480, 367, 234, 126, 57, 22, 6, 12, 22, 33, 43, 47, 43, 33, 22, 12, 6, 3, 3, 4, 8, 14, 24, 36, 46, 50, 46, 36, 24, 14, 8, 4, 3, 3, 7, 13, 23, 34, 44, 48, 44, 34, 23, 13, 7, 52, 112, 206, 321, 419, 458, 419, 321, 206, 112, 52, 3, 4, 8, 14, 24, 37, 47, 52, 47, 37, 24, 14, 8, 4, 3, 3, 7, 14, 24, 37, 48, 52, 48, 37, 24, 14, 7, 3, 10, 17, 29, 42, 54, 58, 54, 42, 29, 17, 10, 3, 7, 13, 23, 35, 45, 49, 45, 35, 23, 13, 7, 3, 4, 4, 5, 9, 16, 26, 39, 50, 54, 50, 39, 26, 16, 9, 5, 4, 4, 4, 7, 14, 25, 38, 49, 53, 49, 38, 25, 14, 7, 4, 7, 14, 25, 39, 51, 55, 51, 39, 25, 14, 7, 7, 10, 17, 27, 41, 52, 56, 52, 41, 27, 17, 10, 7, 6, 19, 50, 112, 210, 329, 430, 471, 430, 329, 210, 112, 50, 19, 6, 2, 6, 18, 49, 109, 204, 320, 419, 459, 419, 320, 204, 109, 49, 18, 6, 2, 55, 121, 224, 351, 458, 501, 458, 351, 224, 121, 55, 5, 9, 15, 25, 37, 48, 52, 48, 37, 25, 15, 9, 5, 2, 3, 7, 13, 23, 36, 47, 51, 47, 36, 23, 13, 7, 3, 2, 4, 7, 13, 23, 34, 44, 48, 44, 34, 23, 13, 7, 4, 3, 5, 8, 15, 27, 41, 53, 57, 53, 41, 27, 15, 8, 5, 3, 1, 2, 6, 12, 23, 35, 46, 50, 46, 35, 23, 12, 6, 2, 1, 6, 12, 23, 35, 46, 50, 46, 35, 23, 12, 6, 4, 8, 14, 24, 37, 47, 51, 47, 37, 24, 14, 8, 4, 2, 7, 21, 55, 124, 232, 363, 475, 520, 475, 363, 232, 124, 55, 21, 7, 2, 4, 7, 14, 25, 38, 50, 54, 50, 38, 25, 14, 7, 4, 1, 2, 6, 12, 23, 35, 46, 51, 46, 35, 23, 12, 6, 2, 1, 7, 13, 23, 35, 45, 49, 45, 35, 23, 13, 7, 2, 7, 22, 57, 113, 209, 326, 426, 465, 426, 326, 209, 113, 52, 22, 9, 5, 6, 12, 22]
},
"height": 100,
"name": "Recombination Rates",
"type": "dataframe"
},
{
"data": [
{
"data": [
[10, 16, 17, 18, 19, 21, 44, 46, 47, 50, 51, 57, 58, 59, 62, 64, 67, 68, 69, 82, 83, 88, 89, 90, 91, 96, 97, 98, 108, 109, 112, 114, 118, 119, 120, 124, 125, 126, 127, 132, 133, 134, 141, 150, 154, 158, 167, 173, 175, 182, 183, 188, 347, 349, 351, 354, 356, 359, 360, 365, 366, 374, 377, 378, 379, 382, 383, 384, 387, 388, 389, 390, 391]
],
"fill": ["blue"]
}
],
"id": "protein_altering",
"name": "Protein Altering",
"type": "marker"
},
{
"data": [
{
"data": [
[121, 196]
],
"dir": "left",
"fill": "rgb(255,255,51)",
"id": "clone-1234567",
"outline": "rgb(0,0,0)"
},
{
"data": [
[371, 400]
],
"dir": "right",
"fill": "rgb(255,255,51)",
"id": "clone-2345678",
"landmarks": [
{
"offset": 157,
"text": "Gap "
},
{
"offset": 137,
"text": "Insertion "
}
],
"outline": "rgb(0,0,0)"
}
],
"name": "Clones",
"type": "box"
},
{
"data": [
{
"fill": "rgb(100,0,0)",
"id": "SNP123",
"offset": 23,
"outline": "rgb(0,0,0)"
},
{
"fill": "rgb(100,0,0)",
"id": "SNP234",
"offset": 45,
"outline": "rgb(0,0,0)"
},
{
"fill": "rgb(100,0,0)",
"id": "SNP345",
"offset": 135,
"outline": "rgb(0,0,0)"
},
{
"fill": "rgb(100,0,0)",
"id": "SNP456",
"offset": 172,
"outline": "rgb(0,0,0)"
},
{
"fill": "rgb(100,0,0)",
"id": "SNP567",
"offset": 180,
"outline": "rgb(0,0,0)"
},
{
"fill": "rgb(100,0,0)",
"id": "SNP678",
"offset": 190,
"outline": "rgb(0,0,0)"
},
{
"fill": "rgb(100,0,0)",
"id": "SNP789",
"offset": 195,
"outline": "rgb(0,0,0)"
}
],
"name": "SNP Location",
"type": "triangle"
},
{
"data": [
{
"id": "SNP123",
"offset": 19,
"sequence": "CACA[AT]GCACCTTGTA"
},
{
"id": "SNP234",
"offset": 41,
"sequence": "ATCG[TG]AATA"
},
{
"id": "SNP789",
"offset": 116,
"sequence": "GCCC[CT]AGGG"
}
],
"name": "SNP Sequences",
"subtype": "DNA",
"type": "sequence"
}
]
},
config = {
"background": "rgb(245,245,245)",
"dataPointSize": 5,
"featureStaggered": True,
"graphType": "Genome"
},
width = 600,
height = 600
)
# Display the chart in its own Web page
show_in_browser(chart)
Run this notebook:
from canvasxpress.canvas import CanvasXpress
from canvasxpress.plot import graph
graph(
CanvasXpress(
render_to = "genome3",
data = {
"tracks": [
{
"connect": True,
"data": [
{
"data": [
[10, 20],
[30, 40],
[50, 60],
[70, 80],
[90, 100],
[110, 120]
],
"dir": "right",
"fill": "rgb(255,255,51)",
"id": "123456_at",
"outline": "rgb(0,0,0)",
"sequences": ["GTTTTACGTAC", "TACGTACGTAC", "GGTTTACGTAC", "GGTTTACGTAC", "GGTTTACGTAC", "GGTTTACGTAC"]
},
{
"data": [
[50, 60],
[70, 80],
[90, 100],
[110, 120],
[130, 140],
[150, 160]
],
"dir": "left",
"fill": "rgb(255,255,51)",
"id": "234567_at",
"outline": "rgb(0,0,0)"
},
{
"data": [
[100, 110],
[120, 130],
[140, 150],
[160, 170],
[180, 190]
],
"dir": "right",
"fill": "rgb(255,255,51)",
"id": "345678_at",
"outline": "rgb(0,0,0)"
}
],
"name": "Affymetrix Probes",
"type": "box"
},
{
"data": [
{
"data": [25, 35, 46],
"id": "123456_at",
"offset": 10
},
{
"data": [80, 45, 10],
"id": "234567_at",
"offset": 50
},
{
"data": [65, 46, 29],
"id": "345678_at",
"offset": 100
}
],
"height": 20,
"name": "Heatmap for Tissue Distribution for Heart (top), Liver (middle), Kidney (bottom)",
"type": "heatmap"
},
{
"data": [
{
"data": [25, 35, 46],
"id": "123456_at",
"offset": 10
},
{
"data": [80, 45, 10],
"id": "234567_at",
"offset": 50
},
{
"data": [65, 46, 29],
"id": "345678_at",
"offset": 100
}
],
"fill": ["rgb(255,0,0)", "rgb(0,0,255)", "rgb(255,255,0)"],
"height": 50,
"name": "Bar graph Tissue Distribution for Heart, Liver and Kidney",
"outline": ["rgb(255,0,0)", "rgb(0,0,255)", "rgb(255,255,0)"],
"type": "bar"
},
{
"data": [
{
"dir": "right",
"fill": "rgb(51,255,255)",
"id": "Reference",
"offset": 1,
"outline": "rgb(0,0,0)",
"sequence": "AAAACCCGGGTTTTACGTACGTACGTACGTACGTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTAAACC",
"translate": [-3, -2, -1, 1, 2, 3]
},
{
"coordinate": 50,
"dir": "right",
"fill": "rgb(255,255,51)",
"gaps": [
[18, 1],
[22, 1]
],
"id": "R1-0000-1234",
"offset": 1,
"outline": "rgb(0,0,0)",
"sequence": "AAAACCCGGGTTTTACGTCGTAGTACGTACGTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAA",
"trace": {
"A": [57, 127, 237, 371, 486, 531, 486, 371, 237, 127, 57, 54, 117, 217, 339, 442, 484, 442, 339, 217, 117, 54, 10, 24, 60, 130, 240, 375, 490, 535, 490, 375, 240, 130, 60, 24, 10, 56, 121, 222, 346, 452, 494, 452, 346, 222, 121, 56, 7, 14, 27, 48, 74, 95, 104, 95, 74, 48, 27, 14, 7, 6, 8, 14, 27, 46, 69, 90, 98, 90, 69, 46, 27, 14, 8, 6, 4, 5, 7, 14, 27, 47, 72, 93, 101, 93, 72, 47, 27, 14, 7, 5, 4, 5, 11, 23, 42, 65, 85, 92, 85, 65, 42, 23, 11, 5, 7, 14, 27, 48, 74, 95, 104, 95, 74, 48, 27, 14, 7, 1, 2, 4, 10, 22, 42, 65, 85, 93, 85, 65, 42, 22, 10, 4, 2, 1, 5, 12, 24, 44, 68, 88, 97, 88, 68, 44, 24, 12, 5, 4, 5, 7, 14, 27, 47, 72, 94, 102, 94, 72, 47, 27, 14, 7, 5, 4, 2, 4, 10, 22, 41, 64, 83, 91, 83, 64, 41, 22, 10, 4, 2, 12, 24, 43, 67, 87, 95, 87, 67, 43, 24, 12, 21, 52, 113, 210, 328, 429, 469, 429, 328, 210, 113, 52, 21, 4, 6, 13, 26, 47, 72, 93, 102, 93, 72, 47, 26, 13, 6, 4, 4, 6, 13, 26, 46, 71, 92, 100, 92, 71, 46, 26, 13, 6, 4, 6, 8, 14, 27, 46, 69, 89, 97, 89, 69, 46, 27, 14, 8, 6, 4, 5, 8, 14, 28, 49, 76, 98, 107, 98, 76, 49, 28, 14, 8, 5, 4, 7, 13, 25, 45, 68, 88, 96, 88, 68, 45, 25, 13, 7, 5, 11, 24, 43, 67, 88, 96, 88, 67, 43, 24, 11, 5, 22, 54, 118, 219, 342, 447, 489, 447, 342, 219, 118, 54, 22, 5, 12, 25, 46, 71, 93, 102, 93, 71, 46, 25, 12, 5, 5, 12, 24, 44, 68, 89, 97, 89, 68, 44, 24, 12, 5, 20, 54, 121, 226, 355, 465, 508, 465, 355, 226, 121, 54, 20, 3, 4, 6, 13, 25, 45, 70, 91, 99, 91, 70, 45, 25, 13, 6, 4, 3, 6, 8, 15, 27, 47, 71, 91, 99, 91, 71, 47, 27, 15, 8, 6, 1, 2, 4, 11, 24, 44, 69, 90, 98, 90, 69, 44, 24, 11, 4, 2, 1, 6, 11, 25, 60, 128, 237, 369, 482, 527, 482, 369, 237, 128, 60, 25, 11, 6, 2, 5, 12, 25, 47, 74, 97, 106, 97, 74, 47, 25, 12, 5, 2, 5, 8, 15, 29, 51, 78, 101, 110, 101, 78, 51, 29, 15, 8, 5, 5, 12, 26, 48, 75, 98, 107, 98, 75, 48, 26, 12, 5, 6, 18, 48, 107, 201, 315, 412, 451, 412, 315, 201, 107, 48, 18, 6, 9, 16, 31, 53, 81, 105, 114, 105, 81, 53, 31, 16, 9, 6, 8, 15, 28, 48, 73, 94, 103, 94, 73, 48, 28, 15, 8, 6, 11, 23, 42, 65, 85, 92, 85, 65, 42, 23, 11, 19, 51, 113, 212, 332, 434, 475, 434, 332, 212, 113, 51, 19, 8, 15, 28, 49, 74, 95, 104, 95, 74, 49, 28, 15, 8, 12, 26, 49, 76, 99, 109, 99, 76, 49, 26, 12, 12, 24, 43, 67, 86, 94, 86, 67, 43, 24, 12, 22, 54, 118, 218, 341, 445, 487, 445, 341, 218, 118, 54, 22, 21, 52, 112, 208, 324, 423, 462, 423, 324, 208, 112, 52, 21, 10, 23, 54, 115, 212, 330, 430, 471, 430, 330, 212, 115, 54, 23, 10, 2, 3, 5, 12, 25, 45, 69, 91, 99, 91, 69, 45, 25, 12, 5, 3, 2, 2, 3, 5, 12, 24, 44, 68, 88, 97, 88, 68, 44, 24, 12, 5, 3, 2, 8, 15, 28, 50, 77, 100, 109, 100, 77, 50, 28, 15, 8, 12, 26, 48, 74, 96, 105, 96, 74, 48, 26, 12, 13, 27, 48, 74, 96, 105, 96, 74, 48, 27, 13, 13, 25, 45, 70, 91, 99, 91, 70, 45, 25, 13, 7, 14, 28, 49, 75, 97, 105, 97, 75, 49, 28, 14, 7, 2, 5, 12, 26, 48, 74, 97, 106, 97, 74, 48, 26, 12, 5, 2, 16, 30, 53, 80, 103, 113, 103, 80, 53, 30, 16, 25, 61, 133, 246, 384, 501, 548, 501, 384, 246, 133, 61, 25, 6, 13, 25, 45, 69, 90, 98, 90, 69, 45, 25, 13, 6, 5, 6, 9, 15, 29, 50, 77, 99, 108, 99, 77, 50, 29, 15, 9, 6, 5, 10, 23, 42, 65, 86, 94, 86, 65, 42, 23, 10, 9, 23, 55, 120, 223, 348, 454, 497, 454, 348, 223, 120, 55, 23, 9, 2, 4, 11, 23, 43, 67, 88, 96, 88, 67, 43, 23, 11, 4, 2, 2, 3, 6, 12, 26, 48, 74, 96, 105, 96, 74, 48, 26, 12, 6, 3, 2, 15, 28, 49, 74, 96, 104, 96, 74, 49, 28, 15, 22, 55, 120, 223, 348, 455, 498, 455, 348, 223, 120, 55, 22, 22, 53, 115, 213, 332, 434, 474, 434, 332, 213, 115, 53, 22, 7, 20, 53, 118, 221, 346, 454, 496, 454, 346, 221, 118, 53, 20, 7, 2, 3, 5, 11, 24, 44, 67, 88, 96, 88, 67, 44, 24, 11, 5, 3, 2, 15, 28, 50, 75, 97, 106, 97, 75, 50, 28, 15, 1, 2, 5, 12, 25, 47, 74, 96, 105, 96, 74, 47, 25, 12, 5, 2, 1, 6, 8, 15, 28, 49, 74, 96, 104, 96, 74, 49, 28, 15, 8, 6, 5, 12, 26, 47, 72, 94, 103, 94, 72, 47, 26, 12, 5, 8, 15, 27, 47, 71, 92, 100, 92, 71, 47, 27, 15, 8, 3, 5, 11, 23, 42, 65, 84, 92, 84, 65, 42, 23, 11, 5, 3, 5, 12, 25, 45, 70, 91, 100, 91, 70, 45, 25, 12, 5, 1, 2, 4, 10, 22, 41, 64, 84, 92, 84, 64, 41, 22, 10, 4, 2, 1, 7, 20, 51, 113, 212, 331, 433, 474, 433, 331, 212, 113, 51, 20, 7, 2, 3, 5, 12, 25, 46, 72, 94, 102, 94, 72, 46, 25, 12, 5, 3, 2, 2, 4, 11, 25, 46, 72, 94, 102, 94, 72, 46, 25, 11, 4, 2, 2, 3, 6, 12, 26, 48, 74, 97, 106, 97, 74, 48, 26, 12, 6, 3, 2, 10, 25, 61, 133, 247, 386, 504, 551, 504, 386, 247, 133, 61, 25, 10, 15, 27, 47, 71, 92, 100, 92, 71, 47, 27, 15, 5, 8, 15, 28, 50, 76, 99, 108, 99, 76, 50, 28, 15, 8, 5, 2, 3, 6, 13, 26, 48, 75, 98, 107, 98, 75, 48, 26, 13, 6, 3, 2, 8, 22, 57, 127, 238, 372, 487, 532, 487, 372, 238, 127, 57, 22, 8, 60, 129, 237, 370, 483, 528, 483, 370, 237, 129, 60],
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"fill": "rgb(255,51,255)",
"id": "R1-0000-3456",
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"sequence": "AAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAAC",
"trace": {
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{
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"gaps": [
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"id": "R1-0000-4567",
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"sequence": "TAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCGGGTTTACGTACGTAAACCG",
"trace": {
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"sequence": "CCCGGTTTACGTACGTAAACCCGGGTTTACGTACGTAAACCCGGGTTTACGTACGTAACCCGGGTTTAAACC",
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"peak": [5, 17, 30, 43, 55, 68, 81, 95, 109, 123, 137, 149, 162, 174, 187, 202, 218, 234, 247, 260, 274, 286, 300, 317, 333, 346, 358, 372, 385, 399, 414, 426, 439, 455, 471, 487, 503, 517, 530, 545, 562, 579, 595, 608, 620, 634, 648, 662, 675, 687, 700, 715, 729, 743, 759, 772, 786, 800, 811, 823, 837, 850, 862, 874, 885, 899, 914, 927, 941, 954, 968, 982]
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