| Read alignment evidence... | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | ref | new | freq | score (cons/poly) | reads | annotation | genes | product | ||
| * | NC_000913 | 3,862,677 | 0 | G | A | 35.7% | 14.8 / 11.9 | 36 | pseudogene (927/1617 nt) | glvC | pseudogene, arbutin specific enzyme IIC component of PTS;enzyme; Transport of small molecules: Carbohydrates, organic acids, alcohols; PTS system, arbutin‑like IIB component; PTS system, arbutin‑like IIC component |
| Reads supporting (aligned to +/- strand): ref base G (6/12); new base A (10/0); total (19/17) | |||||||||||
| Fisher's exact test for biased strand distribution p-value = 8.83e-04 | |||||||||||
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.02e-02 | |||||||||||
| Rejected as consensus: Frequency below/above cutoff threshold. | |||||||||||
GCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTA‑GTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑GGTTGCGGGAATCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGTAGATGAAGTGGTGTA > NC_000913/3862456‑3862912 | gcgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTA‑GTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑AGGTGCGGGGAACAGCAAACCCCCCCC‑CTTTTAccc > 1:1995638/1‑239 (MQ=255) gTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTA‑GTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGGAATT‑CCCACCAGCATGGCGGGTAAGGGTTGGGGGGA‑CAGC‑AAAACCCCCACCTTTTACCGCAttt > 1:1053530/1‑239 (MQ=255) cTGAACATCGGGATCCAGTTTTGCGGTAAAACCTA‑GTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGGTAA‑AGTTTGGGGGAACAGCAAACCCCCCCC‑CTTTTACCCAAttt > 1:1162710/1‑235 (MQ=255) tCCAGTTTTGCGGTAAAACCTA‑GTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑AGGTGCGGGGATCAGC‑AAAACCGCCC‑CCTTTACCCCGGTTTTCGGTGCGGCAGGGAAg > 1:1634939/1‑239 (MQ=255) catttgggctaaaaaCCTATGACAATCACCCCCCCCCACTTGTCCCCCCCCACACAAAAGAGATACATTAGGGTCGACATGGGGGCCGCCAGCGGGGCGTGCCCCCAAAACAGAACGGGAAAAAGGAAAAGGAAGAAAAAT‑CCCGGGGGTTGGTTATCC‑CCCACCAGCATGGGGTTTAA‑GGTGGCGGAAATCAGA‑AACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑Ta < 2:1995638/228‑1 (MQ=255) aaaCCTA‑GTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGGTAA‑GGTGGCGGGGATCAGG‑CAACCCCCCA‑CATTTTCCCGCCTTTTCGGTGCGGGCGGGCAG‑GACAACGCTAAAGaa > 1:2159286/1‑239 (MQ=255) cTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTTA‑AGGTGCGGGGATTAGC‑AAACCCGCCC‑CCTTTTcc > 1:186736/1‑182 (MQ=255) cGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTTA‑AGGTGCGGGGAACAACAAACCCCCCCC‑CTTTTCCCCACTTTTCCGG‑GCGGGGGGGAAGAAACATCCCTAAAAAAATACCCACgcgccaaacaca > 2:2164523/1‑228 (MQ=255) cccacacaaAAGAGACAATTTGGGGCAGACGTGGAGGCCGCAGGCAGGGCGTGTACCGAAAACAGAAGCGGTAAAATGAACAGGAAGGTAACT‑CCCGGCGGTTCGATACTC‑CCCACCAGCAGGGGGGTTAA‑GGTGGCGGAAATAAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTg < 2:2177206/238‑1 (MQ=255) agaTACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTTA‑GGGTTCGGGGATCAGC‑AAACCCGCCC‑CTTTTTCCCCATTTTTCGGGGCGGCAgggga > 1:1645055/1‑172 (MQ=255) cAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑AGGTGCGGGAATCAGC‑AAACCCCCCA‑CTTTTACCCCATTTTCCGGTGCGGCAGAGAAG‑GACATCCCTAAAAAAAATACCACCGCACCAAAGATTTTTGAGTTAACGGGCAGGGGAAAAACGCCTTCCCGGAAAAAAGATTTTAGCGGGT‑CCGCGCCCCAAcacaa > 2:1351939/1‑234 (MQ=255) aGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑GGGTGCGGGGATTAGC‑CAACCCGCCC‑CTTTTTCCCGAATTTTCGGTGCGGGAGGGGAG‑TACATAGCTAAAAAAAAACCCCCGGCACCAAAGAGTTTTTAGGTTCCGCGCCGGGCAAAACCGCCTCTCGGGGACAAAGAATTCAGCGGGTCCGGGGCCCAAACGGAAc > 2:1354159/1‑235 (MQ=255) aaCGGTAAAATGAACAGGAAGGTAAAT‑CCCGGCGTTTCGTTAATC‑CCCACCAGCAGGGCGGTTAG‑GGTGGGGGAAATCAGC‑AGGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAg < 1:1642043/239‑1 (MQ=255) aaTGAACAGAAAGATAATT‑TCAGGGGTTTCGATAATC‑CCCCCCAGCAGGGGGGTAAA‑GTTTGGGGGAATCAGC‑AATCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTgcg < 1:1448401/239‑1 (MQ=255) aaagaaggggaGGGAAAA‑TCCCGGGGTTTGGTTATTCCCCACCGGGTTGGCGGTTAG‑GGTTGCGGAAATCAGC‑AGCCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTgcg < 1:1351939/229‑1 (MQ=255) tGAAGAGGAA‑GTAAATCCCCAGCGGTTGGGTAACC‑CCCCCCAGCGGGGCGGTAAA‑GGTGGGGGAAATCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGcc < 1:609464/239‑1 (MQ=255) agAACAGGAAGAAAAAT‑CCCAGGGTTTCGTTAATC‑CCCACCAGCTTGGCGTTTAG‑GGTGGCGGAAACCAGC‑AACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAg < 1:1319188/228‑1 (MQ=255) aatgTAAAT‑TCCAGCGGTTCGGTATTT‑CCCCCAAGCAGGGCGGTTAA‑GTTTGCGGGAATCAGC‑ACGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGcc < 1:1652388/228‑1 (MQ=255) aagtaaaaT‑CCCGGGGGTTCGTAAATC‑CCCACCAGCAGGGCGGTAAA‑GGTGGCGGGAACCAGA‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTgcg < 1:1279711/224‑1 (MQ=255) gTAAAT‑CCCGGGGGTTCGGTAATC‑CCCCCCAGCTTGGTGGTTAG‑GGTTGGGGAAAACAGC‑AGGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGc < 1:2101132/158‑1 (MQ=255) atccccgctgTTGGGTAATC‑CCCACCAGCAGGGCGGTTAG‑GGTTGCGGAAACCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATg < 1:1354159/230‑1 (MQ=255) gCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTTA‑AGTTTCGGGGATCAAC‑AAACCCGCCA‑CTTTTATCCCATTTTCCCGGGCGGGAGTGAAG‑TACATTGCCAAAGAAAAACCCACGGCCCCAAAAATTTTTTGGGTACCGTGCCGGGCAAAACCCCCt > 2:2101132/1‑158 (MQ=255) gCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑GGTTGCGGGGATCAGC‑AAACCCGCCC‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCg > 1:2162978/1‑99 (MQ=255) gCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑AGTTTCGGGGAACAGC‑AAACCCCCCA‑CTTTTTTCCGAATTTCCg > 1:1840736/1‑78 (MQ=255) ttCGGTAATC‑CCCACCAGCAGGGGGTTAAA‑GGTTGGGGAAATCAAA‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGAt < 1:888786/123‑1 (MQ=255) tcccccccAGCAGGGCGGTAAA‑GGTGGCGGGAATCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTa < 1:1811466/123‑1 (MQ=255) ccccccAGCAGGGGGTTTAG‑GGTTGCGGAATGCACC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGaa < 1:874433/93‑1 (MQ=255) ggtatga‑GGTGGCGGGAATCAGC‑AACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATaaa < 2:1053530/232‑1 (MQ=255) ggggaaaacAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGTAGa < 1:476818/230‑1 (MQ=255) cGGGAATCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGTAGATg > 1:1887684/1‑239 (MQ=255) cGGGAATCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGACCTCAACAACTGCCGGACCCAAGATAAACTGTCCgca > 2:1398554/1‑233 (MQ=255) aaTCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGTAGATGAAgt > 1:901009/1‑239 (MQ=255) aTCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACa > 1:657419/1‑52 (MQ=255) aTCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAg > 1:2223013/1‑177 (MQ=255) aTCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAg < 2:2223013/177‑1 (MQ=255) c‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAAATGTCCGTAGATGAAGTGGGGTa > 1:489100/1‑239 (MQ=255) gCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGTAGATGaa > 1:2087295/1‑228 (MQ=255) gCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGTAGATGaa < 2:2087295/228‑1 (MQ=255) | GCGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACCTA‑GTCAATCAGACCTCCGCCCATGTTGCCCACCACACCAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAAT‑TCCAGCGGTTCGGTAATT‑CCCACCAGCATGGCGGTTAA‑GGTTGCGGGAATCAGC‑AAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAG‑TACATCGCTAAAGAAATGCCCACGGCACCAAAGATTTTTGAGTTACCGTGCAGGGCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCT‑CGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCAAAGATAAACTGTCCGTAGATGAAGTGGTGTA > NC_000913/3862456‑3862912 |
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 9 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |