| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 172,772 | 0 | A | G | 59.0% | 29.3 / 41.3 | 40 | G393G (GGA→GGG) | clcA | H(+)/Cl(‑) exchange transporter ClcA |
| Reads supporting (aligned to +/- strand): ref base A (4/12); new base G (23/0); total (28/12) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 4.65e-07 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.45e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAGATGACCGATAACTACCAGCTCATTTT > NZ_CP009273/172689‑172861 | gtgCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTTCTATTTCCGGGATgggg > 1:509556/1‑90 (MQ=255)gtgCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTTCCGGGATgggg > 1:458158/1‑90 (MQ=255)gtgCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTTTTGTCGGGATgggg > 2:326329/1‑90 (MQ=255)gtgCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTGCCGGGATgggg > 2:576504/1‑90 (MQ=255) cTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTTTTGCCGGGATgggggga > 1:328260/1‑88 (MQ=255) cTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTTCCGGGATGGGGGCa > 2:64101/1‑90 (MQ=255) cTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGAGATTTGTATTTCCGGCAAgggggga > 1:403672/1‑88 (MQ=255) cTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGGTATTTCCGCGGTgggggta > 1:397592/1‑88 (MQ=255) gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGTTTTTTTTTGCCGGGGTGGGGGCGtt > 2:701936/1‑90 (MQ=255) gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTTTTGCCGGGATGGGGGGAtt > 2:558797/1‑90 (MQ=255) gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTTCCGGGATGGGGGGAtt > 1:521533/1‑90 (MQ=255) gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTTTTATTTCCGGGATGGGGGGAtt > 1:339150/1‑90 (MQ=255) gggAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTGCCGGGATGGGGGGAtt > 2:324037/1‑90 (MQ=255) ccGCTTTCGGGATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATGGGGGGATTACTgg > 2:271303/1‑90 (MQ=255) ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGGTTGCTTTTTTCGGGATGGGGGGGTTACttg > 2:398533/1‑88 (MQ=255) ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGGTTGCTTTTGCCGGGATGGGGGGGTTACTgg > 2:635635/1‑90 (MQ=255) ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGGTTGCTATTGCCGGGATGGGGGGGTTACTgg > 2:329405/1‑90 (MQ=255) ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTTCTATTGCCGGGATGGGGGGATTACTgg > 1:341986/1‑90 (MQ=255) ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTATTGCCGGGATGGGGGGATTACttg > 2:471426/1‑88 (MQ=255) ccGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGAGTTTGCTATTTTCGGGATGGGGGGGTTACTgg > 1:135585/1‑90 (MQ=255) gCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGGGGTTGGTGTTTTCGGGGTGGGGGGATTACTggcg > 2:39866/1‑90 (MQ=255) gCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGGTTGCTATTGCCGGGATGGGGGGATTACTggcg > 1:639414/1‑90 (MQ=255) tGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTcgcgc < 1:324037/90‑1 (MQ=255) ccGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCgcgcgc < 1:368197/90‑1 (MQ=255) gAGCTGTTTCCGCAATATCACCTTGAGGCGGGGGCGTTTGCTTTTTCCGGGATGGGGGGATTACTGGCGGCATCTATTTGCGCGCCGGTa > 2:271978/1‑90 (MQ=255) gTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGGATGGGGGGATTACTGGCGGCCTCTATTTGCGCGCCGGTTACggg > 1:510316/1‑90 (MQ=255) tttCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACgggg < 2:509556/90‑1 (MQ=255) tttCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACgggg < 1:209659/90‑1 (MQ=255) ccGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGTGGCATCTATTCGCGCGCCGTTAACGGGGATc < 2:326312/90‑1 (MQ=255) ccGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATc < 1:705541/90‑1 (MQ=255) ccGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATc < 2:423489/90‑1 (MQ=255) ccGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATc < 1:282469/90‑1 (MQ=255) atatCGCCTTGAGGCGGGGACGTTTGCTGTTGCCGGAATGGGGGCTTTACTGGCGGCATCTATTAACGCGCCGTTAACGGGGATCAttct < 2:659660/90‑1 (MQ=255) atatCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCAttct < 1:701936/90‑1 (MQ=255) tatCACCTTGAGGCGGGGGCGTTTGCTATTTCCGGAATGGGGGGATTAATGGGGGCATCTATTCGCGCGCCCGTAACGGGGGTCAttctg > 1:110438/1‑90 (MQ=255) tatCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGGTCAttctg > 1:161489/1‑90 (MQ=255) gAGGCGGGGGCGGTTGCTATTTCCGGAATGGGGGGATTTCTTGCGGCATCTTTTTGCGCGCCGTTAACGGGGGTCATTCTTGTTTTGgag > 2:8240/1‑90 (MQ=255) gggACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAGATGAcc < 2:234138/90‑1 (MQ=255) gggACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAGATGAcc < 1:558797/90‑1 (MQ=255) cGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAGATGACCGATa > 2:207549/1‑90 (MQ=255) aaTGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAGATGACCGATAACTACCAGCTCAtttt > 2:99388/1‑90 (MQ=255) | GTGCTGGGAACCGCTTTCGGAATGGTTGCCGTTGAGCTGTTTCCGCAATATCACCTTGAGGCGGGGACGTTTGCTATTGCCGGAATGGGGGCATTACTGGCGGCATCTATTCGCGCGCCGTTAACGGGGATCATTCTGGTTCTGGAGATGACCGATAACTACCAGCTCATTTT > NZ_CP009273/172689‑172861 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 5 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |