| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP006584 | 1,563,136 | 0 | T | C | 36.0% | 16.5 / 18.3 | 27 | N139N (AAT→AAC) | LY180_07445 | transposase IS609 |
| Reads supporting (aligned to +/- strand): ref base T (7/9); new base C (4/5); total (11/16) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAAAACAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGGCAGAAGCAGAAACGCAAAATACAGCGACT > CP006584/1563086‑1563432 | gAAAACAGTCGGTTGTTTCTGGCGAAATTGGGCGGGATGCGGTTCCGGAATAGCCGT‑CAGGTCACGGGGGTTGTAAAAAATGTCCCTGTACGCCAGGTCTGCGGTAAGTGGTACATCATTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTGCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAgg < 2:9200/298‑1 (MQ=11)gAAAACAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGTGCTACCGGAACAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTAAATCAGTATTCAGACAGAAAGTGAAGTATCCACTACGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGAGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTATTTGAGCCTGTACACAGTTTTCAGAAAAACAAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAgg > 1:369776/1‑298 (MQ=255)gAAAACAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAACAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAgg < 1:543988/298‑1 (MQ=14) aaaaCCGCCGTTTTTTTCGGCCGAAACTGGGCTGGAGGCGCTACCGGAACAGCCTG‑AAGGTCACGGGTGTGGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCATACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGt < 2:397505/298‑1 (MQ=11) aaaaCAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCTCTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTTAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGt < 1:395867/298‑1 (MQ=14) aaaaCAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGt < 1:93296/298‑1 (MQ=31) aaaaCAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAACAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGt < 1:2525/298‑1 (MQ=14) aaCAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCa > 1:602500/1‑298 (MQ=31) cgggcGTTTTTTTCAGCTGGAGCGGGGCTGGATGCGTTAACGGAAGAGCCGC‑CAGGTCACGGGTGTGGTGAAAAATGTGAGTGTCAGGCAGGCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGGGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTGTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCaaa < 2:898232/294‑1 (MQ=11) cAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCaaa > 1:515278/1‑298 (MQ=31) gCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAACAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCCATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACCCTGCCCGATGGCACAGTCTCTGAGCCTGTAAACAGTCTCAAGAAAAACCCAAAGACCCCGGCCAAACTCCACACACAGTTCAGCCGCAAGGTCAAAtt > 2:235619/1‑298 (MQ=11) cGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCa < 1:637436/298‑1 (MQ=31) cGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCa < 1:972315/298‑1 (MQ=31) cGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTAAGCGAGTCCTGCGGTAAGTGGTACATCAGTATTAAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGATTTCAGAAAAACCAGAAGACGCTGACGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAAttaa > 1:613727/1‑296 (MQ=9) gTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAg < 1:977666/298‑1 (MQ=31) cTGCCGAAACTGGGTTGGATGCGCTACCGGAACAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACt < 1:176053/298‑1 (MQ=14) aagtGGGCTGGATGCGCTACCGGAACGGCCGT‑TAGGTCAGGGGGGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGgcagaa < 2:677563/295‑1 (MQ=9) aaCTGGGCTGGATGCGCTACCGGAACAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAGCAACTGgcagaa > 1:553186/1‑298 (MQ=14) ggCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTCTCCACTCCGGTTCACCCTTCAGCATCAATGGTCCGGCTGGCTCCTTGCGTGGCTACACTCGCCAGGCTGTCAGATGGCACATCCTTTGAACCCGTCAACATTTTTCATAAAAACCAGAAGACCACGGCGAGACTTCAGCGAACGTTAAGCCGCCAGGTCAAATTAAGCAACACCTGgcagaaaccaa > 2:244295/1‑293 (MQ=11) cTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGCCAAATTCAGCAACAACTGGCAGAAGCAGaaa < 1:585032/298‑1 (MQ=14) ggATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAACCGCAAGGGCACATTCAGCAACCACCGGCAGAAGAAGaaaac > 2:67292/1‑296 (MQ=9) gATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGACGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGCAAACAGTTGTCAGAACAACCAGAAGACACTGGCGAGACGTCAGACAAATTTAAGCCGCAAGGGCAAATTCAGCAACAACGGGCCGAAGACGAAACga > 2:635333/1‑297 (MQ=11) ggggccaggAAGAGCCGTGCAGG‑CACGGGGGTTGTGAAAAATGGCACTGTCAGCCGGGCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCGTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGGCAGAAGCAGAAACGCaaaa < 2:108534/291‑1 (MQ=11) gcTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGGCAGAAGCAGAAACGCAAAAt > 1:301320/1‑298 (MQ=31) tACCGGAACAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGCTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGGCAGAAGCAGAAACGCAAAATAc > 1:100388/1‑298 (MQ=14) aCCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGGCAGAAGCAGAAACGCAAAATACa < 1:66143/298‑1 (MQ=31) aTAGCCGT‑CAGGTCACTGTGGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTAAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGGCAGAAGCAGAAACGCAAAATACAGCGACt < 1:237493/298‑1 (MQ=14) | GAAAACAGCCGTATTTTTCTGCCGAAACTGGGCTGGATGCGCTACCGGAATAGCCGT‑CAGGTCACGGGTGTTGTGAAAAATGTCACTGTCAGCCAGTCCTGCGGTAAGTGGTACATCAGTATTCAGACAGAAAGTGAAGTATCCACTCCGGTTCACCCTTCAGCATCAATGGTCGGGCTGGATGCTGGCGTGGCTAAACTCGCCACGCTGTCAGATGGCACAGTCTTTGAGCCTGTAAACAGTTTTCAGAAAAACCAGAAGACGCTGGCGAGACTTCAGCGACAGTTAAGCCGCAAGGTCAAATTCAGCAACAACTGGCAGAAGCAGAAACGCAAAATACAGCGACT > CP006584/1563086‑1563432 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |