| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NZ_CP009273 | 3,659,062 | 0 | C | A | 53.8% | 20.7 / 45.4 | 26 | A37S (GCG→TCG) | gadX | acid resistance transcriptional activator GadX |
| Reads supporting (aligned to +/- strand): ref base C (11/1); new base A (0/14); total (11/15) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.55e-06 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.92e-05 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658973‑3659138 | gAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGc > 2:184493/1‑90 (MQ=255) aTCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCaaaa > 2:495191/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACATGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:469498/1‑90 (MQ=255) tCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCaaaaa > 2:555556/1‑90 (MQ=255) aatGAAAGCGTGTCCCTTGACACGAATAAAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGAAAAAACCAGGTCACCg < 1:500/90‑1 (MQ=255) tGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGcc > 1:564724/1‑90 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 2:415505/1‑90 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 2:371120/1‑90 (MQ=255) aaGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCAtt > 1:226725/1‑90 (MQ=255) gtgtCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTaaaa > 1:533763/1‑90 (MQ=255) tgccccTTGACACAAAAAAAAAATTTCCAACACAC‑TTATCTCCTCGATTTTGGCTTGCACCCGAAAAACCCAGGCCACCGCCATTAAAAt < 1:375460/87‑1 (MQ=255) cctttGACACAAATAAAAAATTTTCAACACAC‑TTATCTACTCGATTTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGc < 1:227637/87‑1 (MQ=255) ccgttGACCCGAATAAAAAATTTTCAACACCC‑TTATCTACTCGAATTTGGTTTGCATCCGAAAAAACCAGATCTCCGCCATTAAAATAGc < 1:75649/87‑1 (MQ=255) cccTTGACACAAATAAAAAATTTCAAACCCTC‑TTTTCTCCTCAATTTTGGTTTGCCCCCGAAAAACCCGGTTCACCGCCATTAAAATAGc < 1:567578/90‑1 (MQ=255) ttGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGat > 2:331338/1‑90 (MQ=255) aaaaaaTTTTCAACCCCCTTTTTTTTCTAAAATTTGGCTTGCACCCAAAAAAACCAGTTCACCGCCATTAAAATAGCGATATTCACCAtt < 1:445511/88‑1 (MQ=255) tCAACACAC‑TTATCTACTCGATTTTGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 1:204360/90‑1 (MQ=255) ccAACACCC‑TTATCTACTAAATTTTGGTTTCCACCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTg < 2:466590/89‑1 (MQ=255) aaCACAC‑TTATCTCCTCAATTTTGGCTTGCATCCAAAAAAACCAGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTgag < 1:375259/90‑1 (MQ=255) ccctttATCTCCTCAATTTTGGCTTGCACCCGAAAAACCCGGGTCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 1:356291/86‑1 (MQ=255) ccctttATCTCCTAAATTTTGGTTTCCACCCAAAAAACCCGGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAat < 2:226725/86‑1 (MQ=255) cac‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAata > 1:555455/1‑90 (MQ=255) ttttATCTACCCAATTTTGGTTTCCACCCAAAAAACCCGGGCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAatat < 2:57548/88‑1 (MQ=255) cTCGATTTTGGCTCGCACCCAAAAAAACCAGCCCCCCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc < 2:399846/90‑1 (MQ=255) cTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTc > 2:298229/1‑90 (MQ=255) tGGCTTGCACCCGAAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:210337/90‑1 (MQ=255) tGGCTTGCACCCAAAAAACCCGGGCCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAc < 1:447624/90‑1 (MQ=255) | GAGCATCGGGAGAAATAATGAAAGCGTGTCCCTTGACACGAATACAAAATTTTCAACACAC‑TTATCTACTCGAATTTGGCTTGCATCCGCAAAAACCAGGTCACCGCCATTAAAATAGCGATATTCACCATTAACCATGGTGAGAATATATTTATGTCTTGCATAC > NZ_CP009273/3658973‑3659138 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 7 ≤ ATCG/ATCG < 28 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |