Frames

This audit displays all reference frames against a specific chromosome. This to show all 12 views of a chromosome are working as expected.

Test Setup

The test code here is hard coded against a specific chromosome. This chromosome selected because it is long, and because it has a length that is not an even multiple of 3 nucleotide bases.

Each of the 12 views of that chromosome are displayed.

Because the antisense side of the DNA molecule trades A and T as well as C and G, there is a natural audit to the table displayed here. Each codon pattern counted on the sense side should see an inverted codon counted on the other side with the same count.

The specific matches change based on the left over nucleotide bases, but the matched count should be there somewhere. If this is true, the Audit column marks OK.

Sequence Frame Audit
Chr: 2
Bases: 242,696,752 Extras: 1 Best Possible Codons: 80,898,917
Sense
5'
rf0 		Sense
5'
rf1 		Sense
5'
rf2 		Sense
3'
rf0 		Sense
3'
rf1 		sense
3'
rf2 		Antisense
5'
rf0 		Antisense
5'
rf1 		Antisense
5'
rf2 		Antisense
3'
rf0 		Antisense
3'
rf1 		Antisense
3'
rf2
Codon # Codon # Codon # Codon # Codon # Codon # Codon # Codon # Codon # Codon # Codon # Codon # Audit
TTT 3,191,809 TTT 3,191,326 TTT 3,194,256 TTT 3,191,326 TTT 3,191,809 TTT 3,194,256 AAA 3,191,326 AAA 3,191,809 AAA 3,194,256 AAA 3,191,809 AAA 3,191,326 AAA 3,194,256 OK
TTG 1,567,086 TTG 1,565,873 TTG 1,567,660 TTG 1,198,587 TTG 1,194,841 TTG 1,195,167 AAC 1,198,587 AAC 1,194,841 AAC 1,195,167 AAC 1,567,086 AAC 1,565,873 AAC 1,567,660 OK
TTC 1,635,601 TTC 1,631,712 TTC 1,634,509 TTC 1,643,872 TTC 1,642,445 TTC 1,642,312 AAG 1,643,872 AAG 1,642,445 AAG 1,642,312 AAG 1,635,601 AAG 1,631,712 AAG 1,634,509 OK
TTA 1,720,903 TTA 1,723,134 TTA 1,722,919 TTA 2,085,559 TTA 2,082,950 TTA 2,083,664 AAT 2,085,559 AAT 2,082,950 AAT 2,083,664 AAT 1,720,903 AAT 1,723,134 AAT 1,722,919 OK
GTT 1,194,841 GTT 1,198,587 GTT 1,195,167 GTT 1,565,873 GTT 1,567,086 GTT 1,567,660 CAA 1,565,873 CAA 1,567,086 CAA 1,567,660 CAA 1,194,841 CAA 1,198,587 CAA 1,195,167 OK
GTG 1,194,197 GTG 1,192,846 GTG 1,194,377 GTG 1,192,846 GTG 1,194,197 GTG 1,194,377 CAC 1,192,846 CAC 1,194,197 CAC 1,194,377 CAC 1,194,197 CAC 1,192,846 CAC 1,194,377 OK
GTC 753,279 GTC 753,245 GTC 754,088 GTC 1,593,819 GTC 1,591,905 GTC 1,594,125 CAG 1,593,819 CAG 1,591,905 CAG 1,594,125 CAG 753,279 CAG 753,245 CAG 754,088 OK
GTA 928,496 GTA 928,298 GTA 928,210 GTA 1,509,530 GTA 1,512,306 GTA 1,510,503 CAT 1,509,530 CAT 1,512,306 CAT 1,510,503 CAT 928,496 CAT 928,298 CAT 928,210 OK
CTT 1,642,445 CTT 1,643,872 CTT 1,642,312 CTT 1,631,712 CTT 1,635,601 CTT 1,634,509 GAA 1,631,712 GAA 1,635,601 GAA 1,634,509 GAA 1,642,445 GAA 1,643,872 GAA 1,642,312 OK
CTG 1,591,905 CTG 1,593,819 CTG 1,594,125 CTG 753,245 CTG 753,279 CTG 754,088 GAC 753,245 GAC 753,279 GAC 754,088 GAC 1,591,905 GAC 1,593,819 GAC 1,594,125 OK
CTC 1,318,037 CTC 1,321,955 CTC 1,319,953 CTC 1,321,955 CTC 1,318,037 CTC 1,319,953 GAG 1,321,955 GAG 1,318,037 GAG 1,319,953 GAG 1,318,037 GAG 1,321,955 GAG 1,319,953 OK
CTA 1,055,289 CTA 1,053,945 CTA 1,054,893 CTA 1,092,866 CTA 1,092,104 CTA 1,091,313 GAT 1,092,866 GAT 1,092,104 GAT 1,091,313 GAT 1,055,289 GAT 1,053,945 GAT 1,054,893 OK
ATT 2,082,950 ATT 2,085,559 ATT 2,083,664 ATT 1,723,134 ATT 1,720,903 ATT 1,722,919 TAA 1,723,134 TAA 1,720,903 TAA 1,722,919 TAA 2,082,950 TAA 2,085,559 TAA 2,083,664 OK
ATG 1,512,306 ATG 1,509,530 ATG 1,510,503 ATG 928,298 ATG 928,496 ATG 928,210 TAC 928,298 TAC 928,496 TAC 928,210 TAC 1,512,306 TAC 1,509,530 TAC 1,510,503 OK
ATC 1,092,104 ATC 1,092,866 ATC 1,091,313 ATC 1,053,945 ATC 1,055,289 ATC 1,054,893 TAG 1,053,945 TAG 1,055,289 TAG 1,054,893 TAG 1,092,104 TAG 1,092,866 TAG 1,091,313 OK
ATA 1,720,693 ATA 1,717,718 ATA 1,720,796 ATA 1,717,718 ATA 1,720,693 ATA 1,720,796 TAT 1,717,718 TAT 1,720,693 TAT 1,720,796 TAT 1,720,693 TAT 1,717,718 TAT 1,720,796 OK
TGT 1,652,421 TGT 1,649,342 TGT 1,648,960 TGT 1,649,342 TGT 1,652,421 TGT 1,648,960 ACA 1,649,342 ACA 1,652,421 ACA 1,648,960 ACA 1,652,421 ACA 1,649,342 ACA 1,648,960 OK
TGG 1,466,835 TGG 1,469,812 TGG 1,467,303 TGG 913,845 TGG 914,333 TGG 916,007 ACC 913,845 ACC 914,333 ACC 916,007 ACC 1,466,835 ACC 1,469,812 ACC 1,467,303 OK
TGC 1,144,379 TGC 1,144,878 TGC 1,145,040 TGC 196,116 TGC 195,637 TGC 195,029 ACG 196,116 ACG 195,637 ACG 195,029 ACG 1,144,379 ACG 1,144,878 ACG 1,145,040 OK
TGA 1,603,030 TGA 1,601,462 TGA 1,600,765 TGA 1,312,539 TGA 1,310,585 TGA 1,310,817 ACT 1,312,539 ACT 1,310,585 ACT 1,310,817 ACT 1,603,030 ACT 1,601,462 ACT 1,600,765 OK
GGT 914,333 GGT 913,845 GGT 916,007 GGT 1,469,812 GGT 1,466,835 GGT 1,467,303 CCA 1,469,812 CCA 1,466,835 CCA 1,467,303 CCA 914,333 CCA 913,845 CCA 916,007 OK
GGG 1,003,317 GGG 1,003,567 GGG 1,004,905 GGG 1,003,567 GGG 1,003,317 GGG 1,004,905 CCC 1,003,567 CCC 1,003,317 CCC 1,004,905 CCC 1,003,317 CCC 1,003,567 CCC 1,004,905 OK
GGC 910,449 GGC 908,595 GGC 908,790 GGC 202,976 GGC 201,936 GGC 202,699 CCG 202,976 CCG 201,936 CCG 202,699 CCG 910,449 CCG 908,595 CCG 908,790 OK
GGA 1,243,684 GGA 1,243,019 GGA 1,242,252 GGA 1,395,599 GGA 1,396,938 GGA 1,396,876 CCT 1,395,599 CCT 1,396,938 CCT 1,396,876 CCT 1,243,684 CCT 1,243,019 CCT 1,242,252 OK
CGT 195,637 CGT 196,116 CGT 195,029 CGT 1,144,878 CGT 1,144,379 CGT 1,145,040 GCA 1,144,878 GCA 1,144,379 GCA 1,145,040 GCA 195,637 GCA 196,116 GCA 195,029 OK
CGG 201,936 CGG 202,976 CGG 202,699 CGG 908,595 CGG 910,449 CGG 908,790 GCC 908,595 GCC 910,449 GCC 908,790 GCC 201,936 GCC 202,976 GCC 202,699 OK
CGC 174,235 CGC 173,966 CGC 173,780 CGC 173,966 CGC 174,235 CGC 173,780 GCG 173,966 GCG 174,235 GCG 173,780 GCG 174,235 GCG 173,966 GCG 173,780 OK
CGA 173,611 CGA 174,010 CGA 174,311 CGA 1,119,616 CGA 1,118,453 CGA 1,119,379 GCT 1,119,616 GCT 1,118,453 GCT 1,119,379 GCT 173,611 GCT 174,010 GCT 174,311 OK
AGT 1,310,585 AGT 1,312,539 AGT 1,310,817 AGT 1,601,462 AGT 1,603,030 AGT 1,600,765 TCA 1,601,462 TCA 1,603,030 TCA 1,600,765 TCA 1,310,585 TCA 1,312,539 TCA 1,310,817 OK
AGG 1,396,938 AGG 1,395,599 AGG 1,396,876 AGG 1,243,019 AGG 1,243,684 AGG 1,242,252 TCC 1,243,019 TCC 1,243,684 TCC 1,242,252 TCC 1,396,938 TCC 1,395,599 TCC 1,396,876 OK
AGC 1,118,453 AGC 1,119,616 AGC 1,119,379 AGC 174,010 AGC 173,611 AGC 174,311 TCG 174,010 TCG 173,611 TCG 174,311 TCG 1,118,453 TCG 1,119,616 TCG 1,119,379 OK
AGA 1,796,772 AGA 1,796,126 AGA 1,795,583 AGA 1,796,126 AGA 1,796,772 AGA 1,795,583 TCT 1,796,126 TCT 1,796,772 TCT 1,795,583 TCT 1,796,772 TCT 1,796,126 TCT 1,795,583 OK
TCT 1,802,858 TCT 1,803,328 TCT 1,801,135 TCT 1,803,328 TCT 1,802,858 TCT 1,801,135 AGA 1,803,328 AGA 1,802,858 AGA 1,801,135 AGA 1,802,858 AGA 1,803,328 AGA 1,801,135 OK
TCG 176,788 TCG 175,853 TCG 176,125 TCG 1,109,527 TCG 1,108,455 TCG 1,108,983 AGC 1,109,527 AGC 1,108,455 AGC 1,108,983 AGC 176,788 AGC 175,853 AGC 176,125 OK
TCC 1,220,145 TCC 1,221,007 TCC 1,220,883 TCC 1,392,526 TCC 1,394,158 TCC 1,392,087 AGG 1,392,526 AGG 1,394,158 AGG 1,392,087 AGG 1,220,145 AGG 1,221,007 AGG 1,220,883 OK
TCA 1,600,072 TCA 1,598,833 TCA 1,601,635 TCA 1,305,902 TCA 1,308,120 TCA 1,305,471 AGT 1,305,902 AGT 1,308,120 AGT 1,305,471 AGT 1,600,072 AGT 1,598,833 AGT 1,601,635 OK
GCT 1,108,455 GCT 1,109,527 GCT 1,108,983 GCT 175,853 GCT 176,788 GCT 176,125 CGA 175,853 CGA 176,788 CGA 176,125 CGA 1,108,455 CGA 1,109,527 CGA 1,108,983 OK
GCG 175,900 GCG 175,579 GCG 174,957 GCG 175,579 GCG 175,900 GCG 174,957 CGC 175,579 CGC 175,900 CGC 174,957 CGC 175,900 CGC 175,579 CGC 174,957 OK
GCC 911,117 GCC 911,055 GCC 910,472 GCC 198,638 GCC 199,917 GCC 199,053 CGG 198,638 CGG 199,917 CGG 199,053 CGG 911,117 CGG 911,055 CGG 910,472 OK
GCA 1,151,517 GCA 1,151,355 GCA 1,152,643 GCA 195,749 GCA 194,463 GCA 195,284 CGT 195,749 CGT 194,463 CGT 195,284 CGT 1,151,517 CGT 1,151,355 CGT 1,152,643 OK
CCT 1,394,158 CCT 1,392,526 CCT 1,392,087 CCT 1,221,007 CCT 1,220,145 CCT 1,220,883 GGA 1,221,007 GGA 1,220,145 GGA 1,220,883 GGA 1,394,158 GGA 1,392,526 GGA 1,392,087 OK
CCG 199,917 CCG 198,638 CCG 199,053 CCG 911,055 CCG 911,117 CCG 910,472 GGC 911,055 GGC 911,117 GGC 910,472 GGC 199,917 GGC 198,638 GGC 199,053 OK
CCC 1,006,419 CCC 1,005,340 CCC 1,007,645 CCC 1,005,340 CCC 1,006,419 CCC 1,007,645 GGG 1,005,340 GGG 1,006,419 GGG 1,007,645 GGG 1,006,419 GGG 1,005,340 GGG 1,007,645 OK
CCA 1,449,046 CCA 1,449,987 CCA 1,449,107 CCA 910,490 CCA 908,810 CCA 910,540 GGT 910,490 GGT 908,810 GGT 910,540 GGT 1,449,046 GGT 1,449,987 GGT 1,449,107 OK
ACT 1,308,120 ACT 1,305,902 ACT 1,305,471 ACT 1,598,833 ACT 1,600,072 ACT 1,601,635 TGA 1,598,833 TGA 1,600,072 TGA 1,601,635 TGA 1,308,120 TGA 1,305,902 TGA 1,305,471 OK
ACG 194,463 ACG 195,749 ACG 195,284 ACG 1,151,355 ACG 1,151,517 ACG 1,152,643 TGC 1,151,355 TGC 1,151,517 TGC 1,152,643 TGC 194,463 TGC 195,749 TGC 195,284 OK
ACC 908,810 ACC 910,490 ACC 910,540 ACC 1,449,987 ACC 1,449,046 ACC 1,449,107 TGG 1,449,987 TGG 1,449,046 TGG 1,449,107 TGG 908,810 TGG 910,490 TGG 910,540 OK
ACA 1,640,462 ACA 1,641,785 ACA 1,641,579 ACA 1,641,785 ACA 1,640,462 ACA 1,641,579 TGT 1,641,785 TGT 1,640,462 TGT 1,641,579 TGT 1,640,462 TGT 1,641,785 TGT 1,641,579 OK
TAT 1,718,853 TAT 1,718,608 TAT 1,718,948 TAT 1,718,608 TAT 1,718,853 TAT 1,718,948 ATA 1,718,608 ATA 1,718,853 ATA 1,718,948 ATA 1,718,853 ATA 1,718,608 ATA 1,718,948 OK
TAG 1,061,192 TAG 1,058,265 TAG 1,058,115 TAG 1,094,578 TAG 1,094,440 TAG 1,096,659 ATC 1,094,578 ATC 1,094,440 ATC 1,096,659 ATC 1,061,192 ATC 1,058,265 ATC 1,058,115 OK
TAC 923,609 TAC 923,948 TAC 922,420 TAC 1,515,640 TAC 1,517,199 TAC 1,514,929 ATG 1,515,640 ATG 1,517,199 ATG 1,514,929 ATG 923,609 ATG 923,948 ATG 922,420 OK
TAA 1,723,165 TAA 1,724,560 TAA 1,723,612 TAA 2,077,450 TAA 2,075,181 TAA 2,077,517 ATT 2,077,450 ATT 2,075,181 ATT 2,077,517 ATT 1,723,165 ATT 1,724,560 ATT 1,723,612 OK
GAT 1,094,440 GAT 1,094,578 GAT 1,096,659 GAT 1,058,265 GAT 1,061,192 GAT 1,058,115 CTA 1,058,265 CTA 1,061,192 CTA 1,058,115 CTA 1,094,440 CTA 1,094,578 CTA 1,096,659 OK
GAG 1,323,526 GAG 1,326,167 GAG 1,324,060 GAG 1,326,167 GAG 1,323,526 GAG 1,324,060 CTC 1,326,167 CTC 1,323,526 CTC 1,324,060 CTC 1,323,526 CTC 1,326,167 CTC 1,324,060 OK
GAC 752,210 GAC 752,424 GAC 752,233 GAC 1,607,569 GAC 1,609,404 GAC 1,609,860 CTG 1,607,569 CTG 1,609,404 CTG 1,609,860 CTG 752,210 CTG 752,424 CTG 752,233 OK
GAA 1,642,735 GAA 1,643,928 GAA 1,641,665 GAA 1,630,655 GAA 1,629,758 GAA 1,630,713 CTT 1,630,655 CTT 1,629,758 CTT 1,630,713 CTT 1,642,735 CTT 1,643,928 CTT 1,641,665 OK
CAT 1,517,199 CAT 1,515,640 CAT 1,514,929 CAT 923,948 CAT 923,609 CAT 922,420 GTA 923,948 GTA 923,609 GTA 922,420 GTA 1,517,199 GTA 1,515,640 GTA 1,514,929 OK
CAG 1,609,404 CAG 1,607,569 CAG 1,609,860 CAG 752,424 CAG 752,210 CAG 752,233 GTC 752,424 GTC 752,210 GTC 752,233 GTC 1,609,404 GTC 1,607,569 GTC 1,609,860 OK
CAC 1,184,040 CAC 1,182,177 CAC 1,182,745 CAC 1,182,177 CAC 1,184,040 CAC 1,182,745 GTG 1,182,177 GTG 1,184,040 GTG 1,182,745 GTG 1,184,040 GTG 1,182,177 GTG 1,182,745 OK
CAA 1,534,321 CAA 1,535,711 CAA 1,534,426 CAA 1,194,325 CAA 1,194,067 CAA 1,194,457 GTT 1,194,325 GTT 1,194,067 GTT 1,194,457 GTT 1,534,321 GTT 1,535,711 GTT 1,534,426 OK
AAT 2,075,181 AAT 2,077,450 AAT 2,077,517 AAT 1,724,560 AAT 1,723,165 AAT 1,723,612 TTA 1,724,560 TTA 1,723,165 TTA 1,723,612 TTA 2,075,181 TTA 2,077,450 TTA 2,077,517 OK
AAG 1,629,758 AAG 1,630,655 AAG 1,630,713 AAG 1,643,928 AAG 1,642,735 AAG 1,641,665 TTC 1,643,928 TTC 1,642,735 TTC 1,641,665 TTC 1,629,758 TTC 1,630,655 TTC 1,630,713 OK
AAC 1,194,067 AAC 1,194,325 AAC 1,194,457 AAC 1,535,711 AAC 1,534,321 AAC 1,534,426 TTG 1,535,711 TTG 1,534,321 TTG 1,534,426 TTG 1,194,067 TTG 1,194,325 TTG 1,194,457 OK
AAA 3,158,414 AAA 3,156,205 AAA 3,157,717 AAA 3,156,205 AAA 3,158,414 AAA 3,157,717 TTT 3,156,205 TTT 3,158,414 TTT 3,157,717 TTT 3,158,414 TTT 3,156,205 TTT 3,157,717 OK

Discussion

Getting this working means quite a bit of tricky code is working OK.

Phil Stone 2022-08-25