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.