| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_hsa_tpiA | 1,544,021 | 1 | . | A | 73.0% | 94.3 / 30.5 | 37 | coding (40/1389 nt) | narU | nitrate/nitrite transporter |
| Reads supporting (aligned to +/- strand): ref base . (6/4); new base A (12/15); total (18/19) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.76e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
ATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGT > NC_000913_3_hsa_tpiA/1543878‑1544159 | aTTGAGATTAACGGTAACTGCGCTAAATAGCATCCCGGCACATAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑A‑aa‑aa > 1:203423/1‑149 (MQ=255) agaTTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑A‑aa‑aaagat > 1:59842/1‑145 (MQ=255) tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTTTTTTCCCAGTAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTtc > 1:160851/1‑149 (MQ=255) tGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑AAAA‑AAGATAACGACTATTTTtc > 1:123272/1‑149 (MQ=255) gcTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCa < 1:607614/149‑1 (MQ=255) aGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATTCAGAGATTTATTCGATCAATATGTCTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCa < 2:637914/149‑1 (MQ=255) aTCCAGACACAGAATTCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTg > 2:525980/1‑149 (MQ=255) tCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTTTGGGCCCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGc > 1:821365/1‑149 (MQ=255) ccAGACACAGAAGGCAAGAAGTAGACCACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGTATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTGCTCATTTTGCAGTGcc < 1:90187/149‑1 (MQ=255) caGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTAGTTTCCCAGAAGGCCGGATTTTCTTGTTTCCATTCG‑C‑G‑AAAA‑AAGATAACGACTATTTTGCTCATTTTGCAGTGCCATATTGt < 2:96447/149‑1 (MQ=255) gaagTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATg < 2:123272/149‑1 (MQ=255) aagTAGACAACTGACTGATATCCAGAGCTTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑A‑AATAAGATAACGACTATTTTTCTCCTTTTGCCGTCCCATCTTGTTCCTCAAATgt > 2:450141/1‑148 (MQ=255) agTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGca < 2:59842/149‑1 (MQ=255) gTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGcac < 1:132138/149‑1 (MQ=255) tgactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTa > 1:599804/1‑149 (MQ=255) tactgaTATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATACCCTCTATCGTGCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTaa < 2:770037/148‑1 (MQ=255) tCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGaaaaaa > 1:368457/1‑149 (MQ=255) ttcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACg > 1:214628/1‑149 (MQ=255) tcGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGa < 2:368457/149‑1 (MQ=255) gCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg > 1:440174/1‑121 (MQ=255) gCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg < 2:440174/121‑1 (MQ=255) atGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg < 1:371756/116‑1 (MQ=255) atGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTgg > 2:371756/1‑116 (MQ=255) tGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGCCGCC‑T‑G‑GC‑GAGAGAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGgcgc < 1:450141/149‑1 (MQ=255) ttttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAAAACGGGGTAAGGGGCaa > 2:503994/1‑149 (MQ=255) tttCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAAt > 2:746875/1‑149 (MQ=255) ttCCTTTATTTTCCCATAAGGCCGGATTTTCGGGTTTCCAGTCG‑C‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATa < 1:767522/149‑1 (MQ=255) ttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTg < 1:628216/67‑1 (MQ=255) ttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTg > 2:628216/1‑67 (MQ=255) ttCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGttatt < 1:682814/149‑1 (MQ=255) ctagagGGCCGGATTTTCTGGTTTCCAGTGG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTACTCACATGCACATATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGa < 2:203423/147‑1 (MQ=255) ccAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑CAA‑A‑AA‑AAGATAACGACTATTTTTCTCATTTTGCATTGCCATATTGTTCCTCACATGCACCCATTGGTAATGAAAAAAAGACAAAACACAAGGTAAGGCGCAATAGCCAGTTATTAGa > 1:426707/1‑149 (MQ=255) ggCCGGATTTTCTGGTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAg < 2:214628/149‑1 (MQ=255) gTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg < 2:260952/77‑1 (MQ=255) gTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTg > 1:260952/1‑77 (MQ=255) gTTTCCAGTCG‑C‑GAA‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGa > 1:684406/1‑149 (MQ=255) tCCAGTCG‑C‑G‑AAAA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGt < 1:191253/149‑1 (MQ=255) | ATTGAGATTAACGGTAACTGCGCTAAATAGCATCCAGACACAGAAGGCAAGAAGTAGACAACTGACTGATATCCAGAGATTTCTTCGAGCAATATGTTTTCCTTTATTTTCCCAGAAGGCCGGATTTTCTGGTTTCCAGTCG‑C‑G‑C‑AA‑AAGATAACGACTATTTTTCTCATTTTGCAGTGCCATATTGTTCCTCACATGCACACATTGGTAATGAAAAAAAGACAAAACACGAGGTAAGGCGCAATAGCCAGTTATTAGAATTAAGGATGAATTGGGTGAAGT > NC_000913_3_hsa_tpiA/1543878‑1544159 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |