| Predicted mutation | ||||||
|---|---|---|---|---|---|---|
| evidence | seq id | position | mutation | annotation | gene | description |
| RA | NC_000913 | 1,428,875 | T→C | pseudogene (80/189 nt) | lomR → | pseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion |
| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 1,428,875 | 0 | T | C | 97.4% | 141.3 / ‑4.2 | 39 | pseudogene (80/189 nt) | lomR | pseudogene, Rac prophage lom homolog,Phage or Prophage Related, interrupted by IS5 and N‑ter deletion |
| Reads supporting (aligned to +/- strand): ref base T (1/0); new base C (20/18); total (21/18) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.74e-01 | |||||||||||
ATGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGAC > NC_000913/1428741‑1429010 | aTGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAg > 2:158477/1‑139 (MQ=255) cgcTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGttt > 1:1071469/1‑139 (MQ=255) gatgatCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg < 1:98347/139‑1 (MQ=255) atgatCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGCCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGt > 2:585560/1‑139 (MQ=255) atCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGc < 1:45057/139‑1 (MQ=255) tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg < 2:493612/134‑1 (MQ=255) tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg > 1:493612/1‑134 (MQ=255) tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc > 2:207233/1‑139 (MQ=255) tctcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGCCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc < 1:585560/139‑1 (MQ=255) tcATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACACACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCAt > 2:334942/1‑139 (MQ=255) cATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCAtt > 1:372749/1‑139 (MQ=255) tCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGata < 2:1057893/139‑1 (MQ=255) tCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGata < 1:992349/139‑1 (MQ=255) cTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTa > 1:1008488/1‑139 (MQ=255) ttCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa > 1:112106/1‑139 (MQ=255) ttCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa < 2:1008488/139‑1 (MQ=255) tCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAg > 1:327759/1‑139 (MQ=255) aCCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGccc > 2:1071093/1‑139 (MQ=255) aaaaCGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc > 2:75968/1‑102 (MQ=255) aaaaCGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGcc < 1:75968/102‑1 (MQ=255) aaaaCGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATGGCTTATGAAGGCCCCGGCAGTGGCGACt > 2:561415/1‑139 (MQ=255) cgacgTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACt < 1:334942/139‑1 (MQ=255) gTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTggg < 2:1071469/139‑1 (MQ=255) gaCGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCg < 2:515595/139‑1 (MQ=255) tCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTtat > 1:676988/1‑139 (MQ=255) cGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTtata > 1:828873/1‑139 (MQ=255) ccACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg < 1:88910/59‑1 (MQ=255) ccACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCg > 2:88910/1‑59 (MQ=255) ccACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAg < 2:676988/139‑1 (MQ=255) cacaGCAACACGTCTCTGGCGTGGGGAGCTGGCACGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGt < 1:457816/139‑1 (MQ=255) cAACACGTCTCTGGCGTGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGa < 2:327759/139‑1 (MQ=255) tGGGGAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAAcaca > 2:489973/1‑139 (MQ=255) gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATg < 2:978087/56‑1 (MQ=255) gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATg > 1:978087/1‑56 (MQ=255) gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAgg > 1:1097169/1‑130 (MQ=255) gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAgg < 2:1097169/130‑1 (MQ=255) gggAGCTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAgt > 2:861269/1‑139 (MQ=255) cTGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTAt > 2:112626/1‑139 (MQ=255) tGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa < 1:822427/52‑1 (MQ=255) tGGCGCGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGaa > 2:822427/1‑52 (MQ=255) gcgcgcAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGAc > 1:838095/1‑139 (MQ=255) | ATGCGCTCCGGATGAATATGATGATCTCATATCAGGAACTTGTTCGCACCTTCCCAAGGGGAAAACGCACGACGTGCTGACCGGAAGTGATGACGGTCGCCACAGCAACACGTCTCTGGCGTGGGGAGCTGGCGTGCAGTTTAACCCGACCGAATCCGTGGCCATTGATATTGCTTATGAAGGCCCCGGCAGTGGCGACTGGCGCACTGACGGTTTCATCGTGGGTGTCGGTTATAAGTTCTGATTAGCCAGGTAACACAGTGTTATGAC > NC_000913/1428741‑1429010 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |