Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	3,862,661	T→G	33.8%	pseudogene (943/1617 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

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,862,661	0	T	G	33.8%	15.0 / 9.0	33	pseudogene (943/1617 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 T (8/13);  new base G (9/2);  total (18/15)
Fisher's exact test for biased strand distribution p-value = 2.78e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.78e-01

CGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑GGTT‑GCGGG‑A‑ATCAG‑CAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCA  >  NC_000913/3862457‑3862881                                                                                                                                                                                                                   |                                                                                                                                                                                                                                         cgTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCC‑GCATGGC‑GGGTAA‑AGGT‑TCGGG‑A‑GTCAG‑AAACgccgccc                                                                                                                                                                                                               >  1:396008/1‑227 (MQ=255)        gCTGAACATCGGGATCCAGTTTTGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGGTAA‑GGGT‑GCGGG‑A‑ATTAG‑AAAACCCCCCC‑CTTTTAc                                                                                                                                                                                                       >  1:126451/1‑228 (MQ=255)                tCGGGATCCAGTTTTGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAATGGTT‑GTGGG‑G‑GT‑AG‑CAAGTCCGCCC‑CCTTTAcaccactat                                                                                                                                                                                               >  2:1581137/1‑220 (MQ=255)                      tCCAGTTTTGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGGTAA‑AGTT‑GCGGG‑G‑ATAAG‑CAAAGCCGACA‑CCTTTTCCCCAATTTCCgcgt                                                                                                                                                                                         >  1:638912/1‑225 (MQ=255)                         aGTTTTGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGCGGGTAAA‑GGTTCGGGGG‑ACAACA‑‑CAACCGCGCCC‑CTTTTCCCCGCTTTTcggtcgg                                                                                                                                                                                        >  2:175385/1‑222 (MQ=255)                            tttACGGAAAAACCTTACCCAAACAGCCCCCCGCCCATTTCCCCCACC‑CACAAAAAGAAAAACATTCCGTACGACATGGAGCCGGCCAGCCGGGCTTGCACCAAAAAAAGCAGCGGTAAAATGAAAAGGAAGATAAATCCCGGCGGTTCGTT‑AATCCCCCCCA‑GCAGGGG‑GGTTAG‑GGTG‑GCGGA‑A‑ATCAG‑CAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCa                                                                                                                                                                                    <  2:395352/228‑1 (MQ=255)                              tGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑AGAT‑GCGGG‑G‑ATCCG‑CAAGACCGCCC‑CCTTTACCCGCATTTCCCGTTCGGccgg                                                                                                                                                                                  >  1:296847/1‑224 (MQ=255)                                                            gCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTTA‑AGGT‑GTGGG‑G‑ATCAG‑GAAACCCGCCC‑CATTTTCCCGACTTTTCGGTGTGGCAATGAAGGACA‑ACGCC‑TAAGAAAAGACCA‑C‑CGc                                                                                                                                                >  2:892810/1‑228 (MQ=255)                                                                  gTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑AGGT‑GCGGG‑A‑ATAAG‑CAAACCCGCCA‑CATTTTTCCCCTTTTTCGGGGCggg                                                                                                                                                                                     >  1:441827/1‑188 (MQ=255)                                                                     gCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGGTTA‑GGGT‑GTCGG‑G‑ATCAA‑CCAAACCCCCC‑CCTTTACCCCATTTTCTGGTGTGGGCGTGGAAGACA‑TAGCTCAAAAAAAAGCCCC‑G‑GGCCCCacaa                                                                                                                                         >  2:1160021/1‑224 (MQ=255)                                                                                                      aCATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCCTGGC‑GGGTAA‑AGGT‑GCGGG‑G‑AACAG‑CAAGCCCCCCC‑CCTTTTCCCCACTTTCCGGt                                                                                                                                                                                          >  1:1247623/1‑149 (MQ=255)                                                                                                      aCATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGCGGGTTAA‑GGTT‑CGGGG‑A‑ACCAC‑AAACCCCCCCC‑CTTTTCCCCGTTTTTCCGGGGGGGCGGGGAGGGAAA‑CCGCT‑AAA‑ACAAGCCCA‑CAGGGCCCAAAA‑ATTTTTAGGTTACCGTGCC‑GGCGCAACAcccct                                                                                                      >  2:1795362/1‑225 (MQ=255)                                                                                                       tgtggAGGCCGCAAGCGGGGGGTGTCCCGAAAAAAGCAGGGGAAAAATGAAAGGGAAGTAAAATCCGGGCGGTGGGGA‑ATTCCCCCCCA‑GCAGGGG‑GTTTAG‑GGTG‑GGGGA‑A‑ATCAG‑AAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTg                                                                                                                                                                                         <  2:1245396/145‑1 (MQ=255)                                                                                                             ggCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGGTAA‑GGGT‑GCGGG‑G‑ATCAA‑CAAGCCCGCCACCTTTTTCCCCGTTTT‑CGGGGGGGCAGTGGAGGACA‑TCGCT‑TAAAAAAAACCCACC‑GGCCCCAAAA‑ATTTTTTGGTT‑CCGTGGACGG‑GGAAAACGCCCTTCCgggc                                                                                              >  2:96574/1‑227 (MQ=255)                                                                                                                 gccAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTTA‑GGGT‑GCCGG‑G‑ATCCGCCAACCCCCCCC‑CTTTTCCCCATTTTTCCGGT‑CGGCCGGGGAGGAAATTCCCT‑AAAAAAAAGCCCC‑C‑GG‑ACCAAAGAATTTTTTGGTTCCCATCAA‑GG‑GCAAAACGCCCTCCCGGGacaa                                                                                           >  2:756708/1‑224 (MQ=255)                                                                                                                       aCGGCGTGTACCAAAAACAGCAAGGGTAAAATGAACGGGAAGGAAATTTCCAGCGGTCCGGT‑ATTCCCCCCCA‑GAATGGC‑GGTTAG‑GGTG‑GGGGG‑A‑ATCAG‑AAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTg                                                                                                                                                                                         <  1:141066/133‑1 (MQ=255)                                                                                                                                aCCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGGTAA‑GGTT‑GCggg                                                                                                                                                                                                                                   >  1:671181/1‑86 (MQ=255)                                                                                                                                 ccGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑GGTT‑GCGGG‑a                                                                                                                                                                                                                                 <  2:670063/86‑1 (MQ=255)                                                                                                                                    cAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑GGTT‑GCGGG‑G‑ATCAG‑CAAGCCCGCCC‑CTTTTTCCCGATTTTCCGGGGCg                                                                                                                                                                                       >  1:49543/1‑122 (MQ=255)                                                                                                                                                                ggTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑GGTT‑GCGGG‑A‑ATCAG‑CAAGCCCGCCC‑CCTTTACCCGATTTTCCGGTGCGGCAGGGAAGTACA‑TCGCT‑AAAGAAAAGCCCA‑C‑CGCACCAAAG‑ATTTTTTAGTTACCGTGCA‑GG‑GGAAAACCGCCCTCCGGGAACAACGATTTCAGCGGCTCCGCGGCCACACTGCAATCtttccgaaggtg                                             >  2:454985/1‑215 (MQ=255)                                                                                                                                                                 gaaatttcgggCGGTCGGGT‑AATCCCCCCAA‑GGTGGGG‑GGTGAG‑GGTG‑GGGGG‑A‑ATCAG‑AAACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGcc                                         <  1:434289/218‑1 (MQ=255)                                                                                                                                                                   taaaggtcagggTTTGGTAAATCCCCACCA‑GCATGGC‑GGTTAA‑GGTG‑GCGGA‑A‑ATCAG‑CAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGcc                                         <  1:1283912/217‑1 (MQ=255)                                                                                                                                                                   aaaTTCCAGCGGTTCGGT‑AATTCCCACCA‑GCGTGGC‑TGGTAA‑GGGT‑GCGAA‑A‑ATCAG‑CAACCCCGCCA‑CTTTTACCCGATTTTCCGGTGAGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGAtgct                                              <  1:731554/221‑1 (MQ=255)                                                                                                                                                                      ctCCGGCGGTTCGGT‑AATCCCCACCA‑GCATGGC‑GGTTAA‑GGTG‑GCGGG‑A‑ATCAG‑CAACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTa                                    <  1:746804/227‑1 (MQ=255)                                                                                                                                                                         cgggggTCCGGT‑AATTCCCCCCG‑GCATGGC‑GGTTAG‑GGTG‑GGGGG‑A‑AAAAG‑AAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCa                                                                                                                                                                                    <  1:632391/84‑1 (MQ=255)                                                                                                                                                                          gtgcggttagT‑AACTCCCACCAGGCTGGGC‑TGTAAG‑GGTG‑GCGAG‑A‑ATCGG‑CAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAg                                      <  2:45698/214‑1 (MQ=255)                                                                                                                                                                                 cGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑AGGT‑GCGGG‑G‑ATCAG‑CAAGCCCGCCA‑CTTTTTCCCGATTTTCCGGTGCGGGAGTGaa                                                                                                                                                                               >  1:200420/1‑85 (MQ=255)                                                                                                                                                                                  ggT‑AATCCCCCCCA‑GCAGGGG‑GTTTAG‑GGTG‑GCGGA‑A‑ACCAG‑AAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAg                                                                                                                                                                              <  2:200078/85‑1 (MQ=255)                                                                                                                                                                                          cccACCA‑GCATGGC‑GGTTAA‑GGTT‑GGGGG‑G‑ATCAG‑CAAGGCCGCCC‑CTTTTACCCCCTTTTTCGGGGCGGGGGGGGAGTAAA‑ACGCC‑AAAGAAATGCCCC‑C‑CGCACCCAAG‑AATTTTTTGTTACCGTGCA‑GG‑GCAAAAACGCCTTCCcgg                                                                                               >  2:1113843/1‑150 (MQ=255)                                                                                                                                                                                           ccacaa‑GCGTGGC‑GGTTAA‑GGTG‑GCGGA‑A‑ATCAG‑AAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGa                                                                                              <  1:1115846/150‑1 (MQ=255)                                                                                                                                                                                                gacagatgggcgTTAA‑GGTTGGCGGG‑A‑ATCAG‑CAATCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAAc               <  1:1162104/216‑1 (MQ=255)                                                                                                                                                                                                          cgTTAA‑GGGT‑GGGGGAA‑ATCAG‑AAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGAc    <  1:939818/227‑1 (MQ=255)                                                                                                                                                                                                           gTTGA‑GGTT‑GCGGA‑A‑ATCAG‑CAACCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCa  <  1:175687/228‑1 (MQ=255)                                                                                                                                                                                                                   |                                                                                                                                                                                                                                         CGTGGTTGCTGAACATCGGGATCCAGTTTTGCGGTAAAACC‑TAGTCAATCAGACCTCCGCCCATGTTGCCCACCACAC‑CAAAGAGATACATTACGGTCGACATTGAGGCCGCCAGCACGGCGTGTACCGCAAACAGCAACGGTGAAATGAACAGGAAGGTAAATTCCAGCGGTTCGGT‑AATTCCCACCA‑GCATGGC‑GGTTAA‑GGTT‑GCGGG‑A‑ATCAG‑CAAGCCCGCCA‑CTTTTACCCGATTTTCCGGTGCGGCAGTGAAGTACA‑TCGCT‑AAAGAAATGCCCA‑C‑GGCACCAAAG‑ATTTTTGAGTTACCGTGCA‑GG‑GCAAAACCGCCTTCCGGGAACAACGATTTCAGCGGCTCGGCGCTCAAACTGAACTCTTGCAGATGCTGCGCCCAGTACATCTGAATGCCGCCTTCAACAGCTGCCGGACCA  >  NC_000913/3862457‑3862881

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 6 ≤ ATCG/ATCG < 8 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑