Codons
This audit counts all the codons in the genome. This is a test of the code that manages the test system itself. Provides a reference for understanding the scale of the genome.
Test Purpose
To make sure that the code for scanning the genome is running correctly.
To display a summary of the entire genome.
Test Setup
Using the sense strand in the 5' direction using reference frame 0 each chromosome is scanned and each codon is counted.
The following table shows the results.
Column Keys
Codon is the standard tripple of nucleotide bases. Sorted on the 3D encoding.
Chr: N is each chromosome.
Totals are the per codon totals.
Codon To Chromosome Counts Audit | ||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Codon | Chr: 1 | Chr: 2 | Chr: 3 | Chr: 4 | Chr: 5 | Chr: 6 | Chr: 7 | Chr: 8 | Chr: 9 | Chr: 10 | Chr: 11 | Chr: 12 | Chr: 13 | Chr: 14 | Chr: 15 | Chr: 16 | Chr: 17 | Chr: 18 | Chr: 19 | Chr: 20 | Chr: 21 | Chr: 22 | Chr: X | Chr: Y | Chr: M | Total |
TTT | 2,896,894 | 3,191,809 | 2,647,367 | 2,747,064 | 2,455,660 | 2,321,910 | 2,108,925 | 1,907,622 | 1,605,599 | 1,687,430 | 1,660,312 | 1,717,912 | 1,485,152 | 1,276,906 | 1,180,313 | 1,055,806 | 936,961 | 1,094,897 | 650,594 | 768,704 | 538,999 | 486,048 | 2,052,705 | 505,905 | 83 | 38,981,577 |
TTG | 1,530,595 | 1,567,086 | 1,276,345 | 1,303,730 | 1,192,457 | 1,122,099 | 1,029,328 | 943,391 | 914,657 | 853,048 | 860,634 | 839,493 | 682,047 | 629,081 | 601,655 | 604,775 | 515,004 | 552,405 | 369,668 | 420,701 | 263,784 | 273,141 | 1,022,121 | 324,252 | 30 | 19,691,527 |
TTC | 1,588,819 | 1,635,601 | 1,354,488 | 1,332,780 | 1,269,930 | 1,174,614 | 1,091,845 | 985,126 | 1,491,467 | 899,108 | 909,906 | 885,788 | 786,195 | 709,119 | 950,232 | 980,036 | 531,754 | 560,609 | 369,620 | 426,496 | 306,209 | 333,563 | 1,062,188 | 287,653 | 88 | 21,923,234 |
TTA | 1,572,069 | 1,720,903 | 1,472,307 | 1,517,638 | 1,328,394 | 1,256,012 | 1,105,118 | 1,033,486 | 866,662 | 885,472 | 882,559 | 922,005 | 853,240 | 674,395 | 596,002 | 499,870 | 432,046 | 557,598 | 262,274 | 362,946 | 287,221 | 231,024 | 1,092,771 | 383,175 | 111 | 20,795,298 |
GTT | 1,136,699 | 1,194,841 | 1,001,088 | 986,010 | 925,189 | 861,414 | 787,009 | 722,608 | 694,816 | 650,580 | 647,970 | 660,042 | 550,045 | 497,847 | 469,497 | 417,903 | 379,562 | 408,174 | 268,210 | 311,428 | 206,893 | 219,448 | 796,824 | 209,758 | 28 | 15,003,883 |
GTG | 1,213,723 | 1,194,197 | 953,433 | 892,211 | 885,123 | 837,952 | 820,447 | 723,971 | 677,252 | 699,765 | 691,413 | 661,576 | 516,630 | 512,766 | 486,178 | 505,368 | 479,004 | 402,044 | 395,526 | 369,146 | 234,227 | 311,319 | 740,319 | 213,180 | 20 | 15,416,790 |
GTC | 775,233 | 753,279 | 607,411 | 561,496 | 549,949 | 521,090 | 494,724 | 453,043 | 391,320 | 426,986 | 421,696 | 415,684 | 341,698 | 323,912 | 342,848 | 322,980 | 277,805 | 241,819 | 217,782 | 218,821 | 150,735 | 179,807 | 470,272 | 141,843 | 34 | 9,602,267 |
GTA | 875,036 | 928,496 | 815,174 | 810,744 | 712,224 | 674,839 | 603,321 | 560,540 | 507,712 | 493,365 | 498,376 | 499,053 | 516,343 | 374,641 | 338,459 | 287,104 | 277,943 | 312,281 | 188,985 | 221,538 | 168,624 | 166,177 | 604,537 | 258,227 | 56 | 11,693,795 |
CTT | 1,575,867 | 1,642,445 | 1,345,967 | 1,339,818 | 1,248,926 | 1,180,972 | 1,074,721 | 990,102 | 863,152 | 898,652 | 916,370 | 888,705 | 726,663 | 666,759 | 630,943 | 568,158 | 535,060 | 555,912 | 377,367 | 434,559 | 283,256 | 290,080 | 1,041,845 | 236,071 | 122 | 20,312,492 |
CTG | 1,643,808 | 1,591,905 | 1,301,353 | 1,154,526 | 1,155,761 | 1,090,549 | 1,060,993 | 956,295 | 857,374 | 925,229 | 938,209 | 898,432 | 711,923 | 686,510 | 668,603 | 647,603 | 650,940 | 507,844 | 497,292 | 484,513 | 302,264 | 420,690 | 966,954 | 279,249 | 52 | 20,398,871 |
CTC | 1,413,936 | 1,318,037 | 1,065,578 | 971,787 | 971,624 | 923,495 | 898,849 | 795,347 | 759,652 | 772,533 | 780,098 | 758,672 | 607,197 | 573,036 | 597,679 | 557,915 | 564,670 | 428,525 | 450,084 | 410,171 | 279,271 | 345,348 | 812,709 | 227,014 | 154 | 17,283,381 |
CTA | 1,017,424 | 1,055,289 | 896,896 | 868,689 | 800,473 | 759,362 | 677,701 | 635,143 | 552,770 | 558,800 | 579,570 | 577,424 | 486,589 | 429,850 | 408,578 | 342,540 | 318,703 | 351,735 | 206,131 | 253,723 | 179,537 | 191,450 | 692,520 | 195,344 | 172 | 13,036,413 |
ATT | 1,977,305 | 2,082,950 | 1,758,783 | 1,825,145 | 1,618,272 | 1,513,398 | 1,364,929 | 1,249,293 | 1,711,043 | 1,086,652 | 1,086,757 | 1,099,008 | 1,043,312 | 848,076 | 1,050,659 | 1,099,539 | 567,924 | 706,181 | 355,747 | 465,753 | 368,008 | 327,914 | 1,341,927 | 548,115 | 127 | 27,096,817 |
ATG | 1,714,814 | 1,512,306 | 1,249,534 | 1,228,837 | 1,134,480 | 1,064,562 | 976,475 | 909,791 | 1,332,889 | 832,828 | 812,010 | 804,115 | 707,683 | 633,052 | 552,856 | 681,592 | 459,362 | 488,012 | 305,695 | 415,871 | 294,239 | 319,005 | 981,744 | 941,860 | 50 | 20,353,662 |
ATC | 1,421,019 | 1,092,104 | 912,304 | 875,872 | 815,861 | 769,792 | 710,734 | 661,614 | 640,480 | 600,681 | 600,988 | 600,145 | 527,833 | 451,738 | 425,299 | 387,476 | 346,841 | 360,092 | 243,901 | 282,384 | 200,755 | 228,873 | 717,246 | 306,605 | 137 | 14,180,774 |
ATA | 1,547,525 | 1,720,693 | 1,558,887 | 1,606,824 | 1,337,772 | 1,263,825 | 1,099,081 | 1,039,257 | 861,111 | 865,962 | 891,240 | 911,099 | 1,084,086 | 685,130 | 610,406 | 463,009 | 427,263 | 576,850 | 265,121 | 363,057 | 324,668 | 290,164 | 1,165,248 | 920,094 | 117 | 21,878,489 |
TGT | 1,566,812 | 1,652,421 | 1,368,547 | 1,347,551 | 1,262,895 | 1,176,402 | 1,088,521 | 997,479 | 870,834 | 911,245 | 903,606 | 889,696 | 805,863 | 683,289 | 630,736 | 567,195 | 522,076 | 558,348 | 399,294 | 441,392 | 309,857 | 336,203 | 1,067,697 | 370,387 | 43 | 20,728,389 |
TGG | 1,751,228 | 1,466,835 | 1,169,561 | 1,078,953 | 1,061,534 | 1,005,532 | 976,099 | 877,382 | 1,318,262 | 869,833 | 856,150 | 803,155 | 598,134 | 631,591 | 588,977 | 616,630 | 611,083 | 482,861 | 462,979 | 480,989 | 293,643 | 384,301 | 909,011 | 787,670 | 40 | 20,082,433 |
TGC | 1,157,223 | 1,144,379 | 923,546 | 858,782 | 846,582 | 795,120 | 774,400 | 692,901 | 701,035 | 660,061 | 657,964 | 632,296 | 495,862 | 489,529 | 481,971 | 452,531 | 438,542 | 372,156 | 328,269 | 340,562 | 213,031 | 279,240 | 721,586 | 232,108 | 44 | 14,689,720 |
TGA | 1,621,607 | 1,603,030 | 1,321,346 | 1,289,872 | 1,199,157 | 1,135,678 | 1,043,636 | 964,997 | 884,039 | 872,376 | 885,227 | 879,700 | 713,976 | 655,563 | 610,772 | 799,919 | 533,633 | 534,706 | 378,367 | 431,505 | 283,487 | 326,141 | 1,019,230 | 368,743 | 62 | 20,356,769 |
GGT | 941,920 | 914,333 | 746,435 | 690,451 | 669,854 | 635,000 | 605,017 | 549,016 | 516,779 | 519,575 | 527,597 | 513,404 | 389,586 | 386,088 | 370,262 | 372,914 | 363,924 | 290,565 | 278,884 | 268,483 | 169,308 | 214,373 | 583,109 | 159,575 | 31 | 11,676,483 |
GGG | 1,085,981 | 1,003,317 | 786,117 | 685,711 | 706,305 | 676,150 | 679,606 | 601,078 | 616,132 | 603,210 | 621,399 | 569,990 | 406,875 | 443,132 | 435,850 | 461,694 | 478,701 | 311,944 | 401,882 | 341,913 | 204,640 | 300,647 | 608,041 | 163,546 | 27 | 13,193,888 |
GGC | 980,888 | 910,449 | 715,167 | 616,252 | 642,911 | 609,579 | 621,560 | 539,930 | 503,943 | 548,713 | 550,526 | 519,065 | 368,454 | 392,066 | 396,819 | 424,279 | 435,358 | 280,301 | 361,461 | 300,342 | 179,867 | 262,777 | 534,097 | 148,569 | 50 | 11,843,423 |
GGA | 1,555,904 | 1,243,684 | 982,413 | 918,144 | 897,946 | 863,162 | 832,250 | 750,153 | 1,291,066 | 738,014 | 730,545 | 675,509 | 513,358 | 548,101 | 493,928 | 502,759 | 517,585 | 429,523 | 388,858 | 418,752 | 259,192 | 338,746 | 757,112 | 849,646 | 36 | 17,496,386 |
CGT | 215,614 | 195,637 | 151,762 | 143,624 | 146,936 | 138,820 | 144,017 | 124,473 | 155,656 | 121,912 | 111,511 | 112,326 | 104,295 | 93,895 | 113,706 | 113,025 | 98,122 | 74,420 | 83,461 | 67,147 | 52,729 | 68,886 | 123,342 | 41,581 | 33 | 2,796,930 |
CGG | 261,251 | 201,936 | 147,437 | 136,987 | 139,971 | 139,259 | 154,030 | 125,059 | 208,787 | 130,880 | 130,995 | 119,197 | 107,440 | 100,582 | 112,297 | 121,572 | 130,009 | 68,053 | 121,805 | 78,033 | 64,770 | 83,818 | 111,778 | 68,363 | 34 | 3,064,343 |
CGC | 209,181 | 174,235 | 128,960 | 115,935 | 120,607 | 119,480 | 129,896 | 105,918 | 112,408 | 112,216 | 105,703 | 106,929 | 96,692 | 86,476 | 97,319 | 99,524 | 109,507 | 59,482 | 106,927 | 65,734 | 55,498 | 68,941 | 96,592 | 25,138 | 37 | 2,509,335 |
CGA | 360,256 | 173,611 | 132,576 | 118,966 | 120,532 | 117,902 | 123,881 | 102,987 | 180,780 | 111,207 | 99,892 | 102,670 | 86,350 | 80,114 | 130,850 | 227,981 | 89,358 | 52,751 | 75,811 | 58,168 | 45,125 | 59,852 | 106,907 | 175,617 | 47 | 2,934,191 |
AGT | 1,279,937 | 1,310,585 | 1,111,141 | 1,069,411 | 993,471 | 941,232 | 866,837 | 787,447 | 725,227 | 719,301 | 717,761 | 722,621 | 623,130 | 544,811 | 520,765 | 477,394 | 434,201 | 441,030 | 307,068 | 345,462 | 231,665 | 259,255 | 839,796 | 250,627 | 58 | 16,520,233 |
AGG | 1,457,842 | 1,396,938 | 1,124,815 | 1,006,788 | 1,008,608 | 959,184 | 927,688 | 836,704 | 781,664 | 806,309 | 820,917 | 790,158 | 565,434 | 592,563 | 562,536 | 563,415 | 572,452 | 449,610 | 447,859 | 428,678 | 248,571 | 350,726 | 854,198 | 302,855 | 61 | 17,856,573 |
AGC | 1,124,349 | 1,118,453 | 890,290 | 819,792 | 806,704 | 766,873 | 735,397 | 670,650 | 583,700 | 634,882 | 642,882 | 613,721 | 453,016 | 453,181 | 437,009 | 436,236 | 446,829 | 369,818 | 331,304 | 336,088 | 190,923 | 244,466 | 664,800 | 157,954 | 97 | 13,929,414 |
AGA | 1,786,686 | 1,796,772 | 1,492,917 | 1,440,081 | 1,374,162 | 1,297,217 | 1,195,381 | 1,092,381 | 951,780 | 994,274 | 1,011,866 | 990,710 | 785,940 | 747,695 | 665,693 | 620,351 | 602,693 | 612,105 | 459,074 | 483,282 | 309,359 | 350,565 | 1,155,878 | 355,527 | 67 | 22,572,456 |
TCT | 1,780,582 | 1,802,858 | 1,497,987 | 1,440,265 | 1,362,690 | 1,291,354 | 1,183,641 | 1,090,550 | 948,652 | 992,234 | 1,016,756 | 1,003,393 | 872,060 | 761,073 | 750,482 | 640,645 | 608,070 | 608,462 | 434,406 | 485,249 | 358,012 | 381,275 | 1,157,606 | 274,313 | 99 | 22,742,714 |
TCG | 363,962 | 176,788 | 128,097 | 123,878 | 124,175 | 119,301 | 126,912 | 105,293 | 180,949 | 113,536 | 100,833 | 96,826 | 88,064 | 81,201 | 140,881 | 231,411 | 94,127 | 59,686 | 77,652 | 58,712 | 45,321 | 56,906 | 105,323 | 153,675 | 41 | 2,953,550 |
TCC | 1,279,670 | 1,220,145 | 988,687 | 902,352 | 909,355 | 847,418 | 820,483 | 736,422 | 1,264,091 | 705,979 | 709,795 | 694,967 | 558,098 | 553,414 | 798,259 | 735,961 | 490,928 | 389,494 | 370,387 | 365,464 | 247,975 | 323,360 | 776,464 | 222,727 | 120 | 16,912,015 |
TCA | 1,778,052 | 1,600,072 | 1,326,767 | 1,278,752 | 1,212,231 | 1,134,506 | 1,065,372 | 963,936 | 886,042 | 892,457 | 883,061 | 868,707 | 747,909 | 658,803 | 630,818 | 640,645 | 525,959 | 533,616 | 396,400 | 426,444 | 285,177 | 323,307 | 1,025,862 | 310,326 | 146 | 20,395,367 |
GCT | 1,121,713 | 1,108,455 | 890,195 | 810,347 | 805,757 | 758,885 | 734,228 | 663,380 | 574,732 | 634,103 | 638,717 | 616,234 | 465,375 | 467,626 | 446,855 | 439,766 | 439,954 | 352,418 | 325,441 | 329,955 | 195,989 | 263,228 | 674,429 | 152,676 | 62 | 13,910,520 |
GCG | 204,067 | 175,900 | 128,179 | 116,376 | 123,331 | 123,909 | 133,030 | 107,507 | 112,728 | 112,814 | 107,548 | 106,077 | 96,252 | 88,093 | 97,773 | 101,903 | 107,524 | 61,924 | 107,946 | 65,516 | 55,437 | 71,906 | 97,026 | 33,487 | 17 | 2,536,270 |
GCC | 979,421 | 911,117 | 715,507 | 615,059 | 641,720 | 610,160 | 627,391 | 538,095 | 503,001 | 548,427 | 546,532 | 517,596 | 369,350 | 388,669 | 401,955 | 424,238 | 435,121 | 277,031 | 364,319 | 299,329 | 180,118 | 258,340 | 533,112 | 128,566 | 93 | 11,814,267 |
GCA | 1,165,307 | 1,151,517 | 925,082 | 867,295 | 844,299 | 801,058 | 767,620 | 701,532 | 705,780 | 662,281 | 661,775 | 631,061 | 484,114 | 476,471 | 462,947 | 448,586 | 447,134 | 390,864 | 328,858 | 346,528 | 206,804 | 264,203 | 710,691 | 249,497 | 60 | 14,701,364 |
CCT | 1,451,828 | 1,394,158 | 1,120,238 | 1,006,463 | 1,013,723 | 969,172 | 934,906 | 835,601 | 782,304 | 812,925 | 826,963 | 787,019 | 571,941 | 582,534 | 587,713 | 579,872 | 580,960 | 442,035 | 458,524 | 423,479 | 254,512 | 339,140 | 850,331 | 209,522 | 174 | 17,816,037 |
CCG | 245,522 | 199,917 | 149,936 | 131,704 | 137,827 | 136,250 | 149,525 | 122,906 | 205,165 | 128,944 | 123,420 | 122,402 | 113,745 | 102,456 | 125,934 | 127,615 | 125,570 | 65,210 | 120,522 | 76,253 | 67,646 | 86,689 | 116,830 | 30,403 | 37 | 3,012,428 |
CCC | 1,090,242 | 1,006,419 | 797,975 | 674,239 | 706,857 | 674,385 | 677,789 | 599,206 | 615,562 | 604,920 | 615,315 | 570,416 | 436,994 | 436,703 | 445,382 | 466,043 | 477,127 | 312,680 | 395,044 | 343,393 | 212,439 | 297,651 | 608,137 | 136,118 | 205 | 13,201,241 |
CCA | 1,502,696 | 1,449,046 | 1,182,665 | 1,053,962 | 1,065,458 | 994,138 | 978,591 | 865,453 | 1,299,598 | 838,381 | 832,260 | 817,999 | 649,475 | 634,853 | 857,716 | 812,424 | 579,794 | 445,106 | 435,432 | 433,285 | 278,977 | 374,500 | 921,639 | 258,164 | 174 | 19,561,786 |
ACT | 1,294,218 | 1,308,120 | 1,103,224 | 1,077,606 | 997,371 | 938,742 | 861,219 | 789,979 | 726,960 | 715,467 | 731,911 | 720,987 | 623,926 | 543,052 | 525,088 | 456,530 | 439,879 | 441,234 | 311,372 | 342,974 | 238,211 | 264,977 | 831,199 | 302,738 | 134 | 16,587,118 |
ACG | 232,321 | 194,463 | 152,456 | 142,917 | 141,713 | 137,937 | 142,484 | 123,638 | 157,982 | 120,945 | 114,553 | 113,993 | 95,717 | 89,769 | 90,780 | 102,449 | 96,054 | 67,627 | 80,915 | 67,495 | 49,742 | 65,807 | 118,133 | 92,195 | 37 | 2,792,122 |
ACC | 942,820 | 908,810 | 752,103 | 676,094 | 664,974 | 641,546 | 614,665 | 551,113 | 519,945 | 525,941 | 527,097 | 510,599 | 409,800 | 380,605 | 369,630 | 361,616 | 360,843 | 286,883 | 279,441 | 266,426 | 171,349 | 217,089 | 578,576 | 146,458 | 175 | 11,664,598 |
ACA | 1,573,713 | 1,640,462 | 1,385,389 | 1,351,611 | 1,242,530 | 1,170,897 | 1,079,212 | 1,001,030 | 867,488 | 898,921 | 902,444 | 905,320 | 807,917 | 669,954 | 627,116 | 552,846 | 526,307 | 563,216 | 383,131 | 429,975 | 303,679 | 328,494 | 1,061,592 | 366,774 | 157 | 20,640,175 |
TAT | 1,551,222 | 1,718,853 | 1,552,536 | 1,594,038 | 1,339,984 | 1,258,527 | 1,097,617 | 1,038,634 | 859,157 | 868,295 | 886,940 | 913,562 | 1,069,273 | 689,962 | 629,399 | 488,584 | 417,902 | 573,795 | 260,120 | 363,550 | 321,831 | 287,157 | 1,172,037 | 841,312 | 106 | 21,794,393 |
TAG | 1,018,431 | 1,061,192 | 889,981 | 880,317 | 807,737 | 773,255 | 685,369 | 638,074 | 552,383 | 563,015 | 580,472 | 573,749 | 477,954 | 432,841 | 379,745 | 335,784 | 322,047 | 356,954 | 222,715 | 260,593 | 176,598 | 182,095 | 690,599 | 233,852 | 81 | 13,095,833 |
TAC | 861,919 | 923,609 | 834,925 | 811,680 | 702,318 | 666,062 | 594,644 | 556,223 | 506,445 | 485,776 | 493,906 | 509,519 | 550,707 | 376,224 | 365,433 | 292,830 | 269,241 | 299,809 | 175,337 | 215,484 | 175,250 | 176,207 | 609,141 | 215,254 | 127 | 11,668,070 |
TAA | 1,580,179 | 1,723,165 | 1,467,171 | 1,516,708 | 1,329,870 | 1,259,096 | 1,107,088 | 1,034,911 | 870,348 | 886,471 | 887,136 | 915,714 | 844,660 | 661,185 | 578,669 | 477,208 | 443,999 | 567,523 | 261,949 | 363,855 | 289,483 | 231,382 | 1,081,959 | 464,157 | 110 | 20,843,996 |
GAT | 1,083,301 | 1,094,440 | 898,698 | 895,082 | 825,191 | 782,385 | 721,821 | 662,262 | 644,554 | 594,340 | 612,676 | 592,676 | 485,643 | 453,001 | 447,479 | 739,572 | 365,147 | 364,212 | 260,671 | 288,995 | 193,946 | 224,228 | 707,716 | 227,646 | 32 | 14,165,714 |
GAG | 1,392,414 | 1,323,526 | 1,067,948 | 966,533 | 965,512 | 924,562 | 901,010 | 797,658 | 764,379 | 773,108 | 778,758 | 753,608 | 548,242 | 571,204 | 554,037 | 576,854 | 556,078 | 435,502 | 450,807 | 412,934 | 242,017 | 331,928 | 814,003 | 233,807 | 32 | 17,136,461 |
GAC | 782,902 | 752,210 | 602,516 | 564,650 | 552,796 | 525,712 | 501,501 | 457,093 | 395,183 | 430,310 | 434,564 | 413,755 | 317,828 | 309,199 | 297,795 | 303,267 | 286,571 | 249,501 | 224,493 | 219,124 | 139,830 | 171,658 | 463,604 | 209,199 | 58 | 9,605,319 |
GAA | 2,065,784 | 1,642,735 | 1,360,058 | 1,338,137 | 1,240,692 | 1,181,717 | 1,069,138 | 995,861 | 1,505,685 | 917,185 | 904,544 | 890,891 | 749,033 | 701,283 | 601,495 | 530,540 | 537,616 | 580,281 | 366,007 | 472,560 | 320,251 | 347,656 | 1,054,709 | 1,079,305 | 71 | 22,453,234 |
CAT | 1,615,511 | 1,517,199 | 1,260,060 | 1,246,006 | 1,147,384 | 1,068,419 | 987,198 | 915,528 | 1,330,992 | 824,044 | 823,163 | 806,007 | 750,372 | 624,559 | 819,294 | 746,853 | 467,316 | 510,254 | 304,215 | 384,482 | 279,246 | 294,127 | 979,389 | 363,613 | 133 | 20,065,364 |
CAG | 1,652,758 | 1,609,404 | 1,277,202 | 1,179,095 | 1,174,442 | 1,103,273 | 1,081,116 | 967,779 | 867,521 | 936,161 | 937,292 | 884,782 | 643,468 | 667,492 | 649,298 | 655,046 | 662,814 | 535,549 | 528,460 | 497,853 | 281,035 | 383,655 | 963,408 | 249,255 | 63 | 20,388,221 |
CAC | 1,208,998 | 1,184,040 | 963,247 | 884,766 | 870,212 | 826,368 | 807,649 | 721,220 | 663,641 | 690,850 | 684,085 | 675,494 | 526,923 | 512,196 | 506,824 | 484,796 | 474,737 | 387,044 | 378,029 | 358,214 | 236,255 | 308,650 | 736,813 | 216,216 | 139 | 15,307,406 |
CAA | 1,545,819 | 1,534,321 | 1,323,857 | 1,240,890 | 1,169,091 | 1,098,746 | 1,011,390 | 928,892 | 896,233 | 837,777 | 838,058 | 853,668 | 768,148 | 635,716 | 604,437 | 564,948 | 479,835 | 499,957 | 333,541 | 397,724 | 278,811 | 304,271 | 1,038,588 | 355,639 | 156 | 19,540,513 |
AAT | 2,416,042 | 2,075,181 | 1,770,957 | 1,802,639 | 1,590,923 | 1,502,382 | 1,341,209 | 1,242,647 | 1,711,445 | 1,105,784 | 1,068,398 | 1,106,068 | 1,060,224 | 847,999 | 741,942 | 655,128 | 552,715 | 679,257 | 344,243 | 492,591 | 397,344 | 358,013 | 1,346,545 | 1,281,356 | 116 | 27,491,148 |
AAG | 1,578,712 | 1,629,758 | 1,385,992 | 1,306,414 | 1,233,105 | 1,170,166 | 1,055,145 | 985,383 | 858,012 | 886,576 | 894,405 | 902,994 | 759,515 | 668,235 | 600,050 | 527,306 | 515,724 | 544,605 | 340,599 | 424,350 | 280,487 | 304,792 | 1,046,808 | 349,331 | 73 | 20,248,537 |
AAC | 1,183,549 | 1,194,067 | 994,206 | 987,179 | 917,097 | 872,128 | 792,477 | 729,167 | 706,589 | 653,101 | 668,610 | 654,249 | 541,374 | 485,589 | 440,409 | 389,274 | 392,521 | 421,427 | 276,423 | 315,277 | 211,856 | 218,614 | 779,766 | 266,635 | 162 | 15,091,746 |
AAA | 2,994,656 | 3,158,414 | 2,731,530 | 2,681,456 | 2,421,178 | 2,300,611 | 2,068,620 | 1,900,953 | 1,592,155 | 1,667,211 | 1,657,953 | 1,730,884 | 1,630,420 | 1,267,042 | 1,115,733 | 940,491 | 927,770 | 1,051,705 | 614,422 | 745,681 | 554,244 | 524,015 | 2,052,716 | 729,542 | 185 | 39,059,587 |
1,039,097,350 | ||||||||||||||||||||||||||
Totals: | 82,795,776 | 80,898,917 | 67,035,316 | 64,524,981 | 60,681,813 | 57,375,542 | 53,522,476 | 48,753,110 | 50,205,749 | 44,919,378 | 45,042,589 | 44,441,516 | 37,855,562 | 33,720,497 | 33,251,065 | 32,110,124 | 28,092,299 | 26,847,512 | 20,569,121 | 22,070,085 | 15,030,227 | 17,108,308 | 51,419,855 | 20,820,009 | 5,523 | 1,039,097,350 |
OK | ||||||||||||||||||||||||||
Expected Vs. Actual Codon Counts | ||||||||||||||||||||||||||
Chr: 1 | Chr: 2 | Chr: 3 | Chr: 4 | Chr: 5 | Chr: 6 | Chr: 7 | Chr: 8 | Chr: 9 | Chr: 10 | Chr: 11 | Chr: 12 | Chr: 13 | Chr: 14 | Chr: 15 | Chr: 16 | Chr: 17 | Chr: 18 | Chr: 19 | Chr: 20 | Chr: 21 | Chr: 22 | Chr: X | Chr: Y | Chr: M | Totals | |
Bases: | 248,387,328 | 242,696,752 | 201,105,948 | 193,574,945 | 182,045,439 | 172,126,628 | 160,567,428 | 146,259,331 | 150,617,247 | 134,758,134 | 135,127,769 | 133,324,548 | 113,566,686 | 101,161,492 | 99,753,195 | 96,330,374 | 84,276,897 | 80,542,538 | 61,707,364 | 66,210,255 | 45,090,682 | 51,324,926 | 154,259,566 | 62,460,029 | 16,569 | |
Expect: | 82,795,776 | 80,898,917.333 | 67,035,316 | 64,524,981.667 | 60,681,813 | 57,375,542.667 | 53,522,476 | 48,753,110.333 | 50,205,749 | 44,919,378 | 45,042,589.667 | 44,441,516 | 37,855,562 | 33,720,497.333 | 33,251,065 | 32,110,124.667 | 28,092,299 | 26,847,512.667 | 20,569,121.333 | 22,070,085 | 15,030,227.333 | 17,108,308.667 | 51,419,855.333 | 20,820,009.667 | 5,523 | 1,039,097,350 |
Processed: | 82,795,776 | 80,898,917 | 67,035,316 | 64,524,981 | 60,681,813 | 57,375,542 | 53,522,476 | 48,753,110 | 50,205,749 | 44,919,378 | 45,042,589 | 44,441,516 | 37,855,562 | 33,720,497 | 33,251,065 | 32,110,124 | 28,092,299 | 26,847,512 | 20,569,121 | 22,070,085 | 15,030,227 | 17,108,308 | 51,419,855 | 20,820,009 | 5,523 | 1,039,097,350 |
Actual: | 82,795,776 | 80,898,917 | 67,035,316 | 64,524,981 | 60,681,813 | 57,375,542 | 53,522,476 | 48,753,110 | 50,205,749 | 44,919,378 | 45,042,589 | 44,441,516 | 37,855,562 | 33,720,497 | 33,251,065 | 32,110,124 | 28,092,299 | 26,847,512 | 20,569,121 | 22,070,085 | 15,030,227 | 17,108,308 | 51,419,855 | 20,820,009 | 5,523 | 1,039,097,350 |
Audit: | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK | OK |
Discussion
The sequence data for each chromosome is a list of nucleotide bases. The total number of those bases is not always an even multiple of 3.
This is ill defined in terms of codon counting. If the length is an even multiple of 3, then the expected number of codons is the number of bases / 3. Otherwise the expected number of codons is rounded down to the nearest whole number. This rounding is leaving off the 1 or 2 extra bases in the chromosome.
The expect row near the bottom of the table above shows the bases / 3. If there is no fractional part then all bases are used in codons. If there is a fractional part, say, .33 or .67 then 1 or 2 bases are extra and should not used. The total for this row is the sum of the rounded down counts of expected codons.
The actual row shows how many bases were actually found when processing the file. This should match the whole number part of the expected value.
The bottom audit row in the table above is showing if this process of ignoring extra bases is actually going on correctly. The whole number part of the expected value should match the actual codon counts listed above. If they do not, then this audit fails.