| Predicted mutation | |||||||
|---|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | freq | annotation | gene | description |
| RA | CP000730 | 1,440,007 | Δ1 bp | 100% | coding (34/201 nt) | cspA ← | cold shock protein CspA |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | CP000730 | 1,440,007 | 0 | C | . | 97.4% | 160.0 / ‑2.0 | 38 | coding (34/201 nt) | cspA | cold shock protein CspA |
| Reads supporting (aligned to +/- strand): ref base C (0/0); major base . (13/24); minor base T (0/1); total (13/25) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.86e-01 | |||||||||||
| Rejected as polymorphism: E-value score below prediction cutoff. | |||||||||||
| Rejected as polymorphism: Frequency below/above cutoff threshold. | |||||||||||
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. | |||||||||||
| Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch. | |||||||||||
GCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT > CP000730/1439873‑1440140 | gctgTCGCCTTCAACTACTTTAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGtt < 1:89443/137‑1 (MQ=255) gacctatacaactTCATACGCAACAGCTTGACCTTCTTCTAATGCGTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACTAATTCGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCa < 2:74247/130‑1 (MQ=255) cacTTCGACTAGTTCAAACTCTCCGGCTTGTCCTTCTTCTATTGATTTGTAACCCTCTTGGTTAATTGCTGAAAAATGTTCGAACACGTCATTTTCTCCTTCAACTTCGTTAAAGCCGAATCCTTTTT‑AGCGTTAAACCa < 2:74271/138‑1 (MQ=255) cTTTAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAtt < 2:119421/140‑1 (MQ=255) cTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAtt < 2:666980/140‑1 (MQ=255) cTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCAtt < 2:666981/140‑1 (MQ=255) ctactTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAACACGTCATTTTCTCCTTCAACTTCGATCAAGCCTAATCCTTTTT‑AGCGTTAAACCATTTAACTg < 1:646418/140‑1 (MQ=255) tcccatttcgtcAGGTTGACCTTTGTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTAcc < 2:147713/129‑1 (MQ=255) cTCAACAGCTTGACCTTCTTCTGCGAAGTGGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGttt > 1:720294/1‑140 (MQ=255) cAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCa > 1:36271/1‑140 (MQ=255) aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAACCGAATCCTTTTT‑GGCGTTAAACCAGTTAACTGTACCTTGTTTCATAAt > 1:132745/1‑140 (MQ=38) aGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTAATTTTTTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGTGTTAAAACTTTTAACTGTACCTTTTTTCATTAt > 1:22723/1‑140 (MQ=38) gCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATc < 1:136010/140‑1 (MQ=255) cTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCt < 2:356270/140‑1 (MQ=255) tGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa > 2:412397/1‑140 (MQ=255) tGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGa > 2:412556/1‑140 (MQ=255) aaTGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGAc < 2:136323/140‑1 (MQ=255) ccATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAattcattc > 1:650578/1‑140 (MQ=255) cTTGGTTAATTGCTGAAAAATGTTCGAATACGTCATTTTCTCCTTCAACTTCGATATAGCCGATTCCTTTTT‑AGCGTTAATCCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAata < 1:3358/140‑1 (MQ=255) cTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAata < 1:603889/140‑1 (MQ=255) aaTTGCTGAAAAAGGTTCGGATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTGCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTAt < 1:487978/140‑1 (MQ=255) aaaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACGTCCACAACTAAAATTCATTCAATATGCTTATTCGCATAtt > 1:377028/1‑140 (MQ=255) aaaaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCACTTTT‑ACCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGACACCTCCACGCCTAAAATTCATTCAATATCCTTATTCGCACAtt > 2:351020/1‑140 (MQ=255) aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTAc < 1:54905/140‑1 (MQ=255) tACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATACTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACaaaa < 2:374199/140‑1 (MQ=255) cGAATACGTCATTTTCTCCTTCAATTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTGTTCGCATATTACaaaaaa > 1:462636/1‑140 (MQ=255) ccTTCAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTAACt > 1:255006/1‑140 (MQ=255) tccaCTTCGATAATGCCGATTTCTTTTT‑AGCGTTTAATCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTCACTCGCATATTACAAAAAAGACATGCAAATTTCACTCaa < 1:472758/137‑1 (MQ=255) cAACTTCGATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCaaa < 1:368790/140‑1 (MQ=255) gATACACCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGACACCTCAAAGACTAAAATTCATCCAATATGCTTATTAGAAAAAAAAAAAAAATACATGCAAATTTCACTCAAATATTCtt < 2:367138/140‑1 (MQ=255) gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTACCTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATCCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCACATTTCACTCAAATATTcgt < 2:718764/140‑3 (MQ=255) gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt > 1:239249/1‑140 (MQ=255) gATAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTCAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCtt < 2:432743/140‑1 (MQ=255) tAAAGCCGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTg < 2:256351/140‑1 (MQ=255) cGAATCCTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAatat < 2:48729/140‑1 (MQ=255) aaTCCTTTTT‑AGCGTCAAACCATTTAACTGTACCTTGTTTCATAATCGGAATCCCCCAAGACTAAAATTCATTCAATATGCTTATTCGCATAGTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg < 2:139253/140‑1 (MQ=255) aattcttttTAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg < 2:33789/135‑1 (MQ=255) ccTTTTT‑AGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGAaat > 2:440255/1‑140 (MQ=255) | GCGGTCGCCTTCAACTACTTCAAACTCAACAGCTTGACCTTCTTCTAATGATTTGTAACCATCTTGGTTAATTGCTGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAAT > CP000730/1439873‑1440140 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |