| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913_3_pae_pgi | 2,866,773 | Δ2 bp | coding (778‑779/993 nt) | rpoS ← | RNA polymerase, sigma S (sigma 38) factor |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913_3_pae_pgi | 2,866,773 | 0 | A | . | 98.0% | 218.0 / ‑2.1 | 49 | coding (779/993 nt) | rpoS | RNA polymerase, sigma S (sigma 38) factor |
| Reads supporting (aligned to +/- strand): ref base A (1/0); new base . (18/30); total (19/30) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.88e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.46e-01 | |||||||||||
| * | NC_000913_3_pae_pgi | 2,866,774 | 0 | C | . | 98.0% | 221.2 / ‑2.5 | 49 | coding (778/993 nt) | rpoS | RNA polymerase, sigma S (sigma 38) factor |
| Reads supporting (aligned to +/- strand): ref base C (1/0); new base . (18/30); total (19/30) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 3.88e-01 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.33e-01 | |||||||||||
CCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTGACGATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAGGTAATGCGCTCGTTAA > NC_000913_3_pae_pgi/2866633‑2866908 || ccTTAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGc < 2:738641/150‑1 (MQ=255)ccTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGc < 1:4896/150‑1 (MQ=255) cTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCt < 1:483910/150‑1 (MQ=255) taaTCTGGCGAACACGTTCAGGGGGGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCTCT‑TCGTACCCCAGAAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTc < 1:527696/149‑1 (MQ=255) gCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGt > 2:535239/1‑150 (MQ=255) acacGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATc < 2:223370/150‑1 (MQ=255) cacGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCt < 1:579090/150‑1 (MQ=255) acGTTCACGGGTGAGGCCAATTTCACGACCTACATCGTCCCGT‑ACGCCAATATCTGGCCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCtt < 1:719435/150‑1 (MQ=255) gTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGc > 1:576306/1‑150 (MQ=255) gCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCg > 1:199028/1‑150 (MQ=255) gCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCg > 1:382530/1‑150 (MQ=255) ccAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTGACGATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTcc > 1:898073/1‑150 (MQ=255) ccAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCgc > 2:634967/1‑149 (MQ=255) aTTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGAcc < 2:677027/150‑1 (MQ=255) tCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGtt < 1:35633/150‑1 (MQ=255) gACCTACCTCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTctct < 1:455172/150‑1 (MQ=255) actaccAGTGTTTGCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATc < 2:488573/146‑1 (MQ=255) ttGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATg > 1:705079/1‑150 (MQ=255) ccAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGATCAGCTCGAACAGCCATTTG‑‑GATGCTCTTCTTCATATCGTCATCTTGCGTGGTATCTTCCGAACCGTTCTCTTTTTCATCGTCCAGGATGTCCACCACCGCgttt > 2:280640/1‑150 (MQ=255) cAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCa < 1:211943/141‑1 (MQ=255) cAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCa > 2:211943/1‑141 (MQ=255) aGCAAACCGAAGCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATAGCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTc < 1:213629/150‑1 (MQ=255) aTCGACCCGCCAGCACTTCACGCTGTTTGGCGTTCAGCCCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCATGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATcacca < 2:256448/150‑1 (MQ=255) tCGCCGTGCCACCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCTGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATcaccac < 2:926026/150‑1 (MQ=255) gCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATc < 1:733924/105‑1 (MQ=255) gCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATc > 2:733924/1‑105 (MQ=255) cACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGgtgt < 1:159037/150‑1 (MQ=255) ttCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTa < 1:499753/150‑1 (MQ=255) tCACGTTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTAc < 2:538016/150‑1 (MQ=255) tCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTAc < 2:571477/150‑1 (MQ=255) gCTGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAg < 2:576306/150‑1 (MQ=255) tGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAgg > 1:476706/1‑97 (MQ=255) tGTTTGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAgg < 2:476706/97‑1 (MQ=255) tttGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTc < 2:135441/139‑1 (MQ=255) tttGGCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTc > 1:135441/1‑139 (MQ=255) ggCGGTCCGCTCGAACCGCCATTTG‑‑GATGCCCTGCTTCCTATCGGCCTCTTGCGTGGTATCTTCCGGACCGTTCTCTTTGTCATCGGCCAGGACGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAGGTAATgc < 1:484323/150‑1 (MQ=255) gCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATc > 2:778032/1‑48 (MQ=255) gCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATc < 1:778032/48‑1 (MQ=255) gCGTTCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTCCGGAATCACCACCCAGCGGGGTGTCTACCTAGGTAATgag > 2:810884/1‑148 (MQ=255) ttCAGCTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAGGTAATGCGCTc > 1:96117/1‑150 (MQ=255) cTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAAc > 2:502916/1‑95 (MQ=255) cTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAAc < 1:502916/95‑1 (MQ=255) cTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAgg > 2:329878/1‑135 (MQ=255) cTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAgg < 1:329878/135‑1 (MQ=255) cTCGAACAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAGGTAATGCGCTCGTTaa < 1:152091/150‑1 (MQ=255) aaCAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTAc > 2:562519/1‑126 (MQ=255) aaCAGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTAc < 1:562519/126‑1 (MQ=255) aGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAGGTAAt < 1:856453/132‑1 (MQ=255) aGCCATTTG‑‑GATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAGGTAAt > 2:856453/1‑132 (MQ=255) || CCTGAATCTGGCGAACACGTTCACGGGTGAGGCCAATTTCACGACCTACATCTTCCAGTGTTGCCGCT‑TCGTACCCCAGCAAACCGAATCGACGTGCCAGCACTTCACGCTGTTTGGCGTTCAGCTCGAACAGCCATTTGACGATGCTCTGCTTCATATCGTCATCTTGCGTGGTATCTTCCGGACCGTTCTCTTTTTCATCGGCCAGGATGTCCAGCAACGCTTTTTCGGAATCACCACCCAGCGGGGTGTCTACCGAGGTAATGCGCTCGTTAA > NC_000913_3_pae_pgi/2866633‑2866908 |
| 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: ‑ |