Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	52.5%	11.1 / 50.7	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/4);  new base A (0/21);  total (15/25)
Fisher's exact test for biased strand distribution p-value = 9.64e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.06e-07

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357743‑358037                                                                                                                                                     |                                                                                                                                                         aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                                       <  2:885222/151‑1 (MQ=255)            gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTtct                                                                                                                                          >  1:193550/1‑151 (MQ=255)            gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTtct                                                                                                                                          >  1:458001/1‑151 (MQ=255)                       ttCCAGCCCCGGCCCTTTGTCAGCGGCTACCGTGATTCTTTCCCGCCAACACCCGCGCTTTTATCCACCGCCAGGTGCAAAAAT‑GCCTCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGAAAAAAAA‑‑CCGCCGTTCTCTCCagtagt                                                                                                                                <  2:331247/150‑1 (MQ=18)                           aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCCGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑g                                                                                                                           >  1:359522/1‑150 (MQ=255)                             ccGCAGCCCTGTTTCAGCGTCTCCCGTGATTCATTCCCGCCAACACCCGCGCTTTTACCCACCGCCATGTGAAAAAAT‑GCTTTCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑gg                                                                                                                          <  2:712959/149‑1 (MQ=21)                                   cccTGTGCCCGGGCCTTCCGTTATTCATTCCCCCCACCACCGGCGCATTTACCCACCACCATG‑ACAAAAATGGCTTTCGCGCCGCTTGCCTCCGTGCTATTTGCCCGCAGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCaa                                                                                                                     <  2:709044/147‑1 (MQ=255)                                     cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑ggggggaga                                                                                                                   >  2:340889/1‑143 (MQ=255)                                     cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                                        >  2:687476/1‑143 (MQ=255)                                           cAGCGGCTACCGTGATTCTTTCCCGCCAACACCCGCGCATTTACCCAACGCCAGGTGAAAAAAG‑GCCTTCGCGGCGGCTGTCGGCCAGTTTTTTTCCCCCCGAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATa                                                                                                           <  2:346348/148‑1 (MQ=255)                                            aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCTCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑ggcgtgcggggaaaaa                                                                                                            >  1:430109/1‑134 (MQ=21)                                             gcgcCTCCCGTGTTTCATTCCCCCCAAAACCCGCCCTTTTACCCACCCCCATGTGAAAAAAT‑CCCTCCGCGGGGGCTGTCGCCCAGTTATTTTCCGGCCGAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAg                                                                                                          <  1:552211/147‑1 (MQ=255)                                                gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAGGG‑G‑aaaaaacatt                                                                                                      >  1:713646/1‑141 (MQ=25)                                                          ttcttcccccccaccaCCCCCGCATTTACCCACCCCTATGTAAAAAAAT‑GCTTTCGCGGCGTCTTTCCCCCGGCTTTTTTCCCGCCAAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCAt                                                                                           <  1:323403/139‑1 (MQ=255)                                                                  cGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑G‑AAAAAAAATTAAACCCCTCAcgtttt                                                                                      >  1:609246/1‑144 (MQ=25)                                                                   gCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCGGA‑GAAAAAAACTTTAAGccggcctgtttgttt                                                                                    >  1:894594/1‑135 (MQ=25)                                                                           ccgcgtttttccccAACCCCATGTAAAAAAAT‑GCTTTCGCGGGGGCTTTCCGCCAGTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCg                                                                            <  1:618580/135‑1 (MQ=255)                                                                            cgcgCTTTTACCCACCGCCATGTGAAAAAAT‑GCCTCCGCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                       <  2:314681/151‑1 (MQ=255)                                                                             gcttaTTTACCCAGCGCCATGTGAAAAAAC‑GCCTTCGCGGCGGTCGTTTGCCTGCGTTTTTACCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GCGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGctgctg                                                                      <  2:850800/147‑1 (MQ=255)                                                                                   ttATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGA‑G‑AAAAAAATTTAAAGCCCTCCTTTTTTGTGGGGATCGctgctg                                                                      >  2:356302/1‑145 (MQ=25)                                                                                   ttATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGAGG‑AAAAAATTTTAAACCCCCCTTTTGTTGGGGCAA‑CGCTGCTGGGAAc                                                                 >  2:621747/1‑150 (MQ=21)                                                                                     acccACCGCCATGTGAAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                               <  2:923186/148‑1 (MQ=255)                                                                                      tCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAAG‑A‑AAAAAACTTTAAACCCG‑CCTGTTGTGTGGGAATCACGACTGGtgaaaa                                                               >  2:607699/1‑144 (MQ=21)                                                                                           ccccATGTGAAAAAAT‑CCCTCCGCGGCGGCTGTCGCCCATCTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                                        <  1:369465/149‑1 (MQ=255)                                                                                           cGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTCCCCGTTTTTTTCCCCCCGAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                                         <  2:324308/150‑1 (MQ=255)                                                                                           cGCCAGGTAAAAAAAC‑CCCTCCGCGGCGGGTGTCTCCCCTTTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTgg                                                          <  1:872645/149‑1 (MQ=255)                                                                                                 tgggcaaaaggcccTTCGCGGCGTTTTTCTCCCTGCT‑TTTTTCC‑CCGCAAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                                                    <  1:302739/138‑1 (MQ=255)                                                                                                     aaaaaT‑GCCTTCGGGGCGGTTGTCTGCCAGCTATTTTTCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                              <  2:104075/151‑1 (MQ=255)                                                                                                     aaaaaT‑GCCTTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                                                <  2:762842/149‑1 (MQ=255)                                                                                                               tccgcgGCGCCTGTCCCCCATCTTTTTTCCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                         <  1:886400/145‑1 (MQ=255)                                                                                                                 cgcgGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCCAGA‑G‑AAAAAAATTTAAACCCCCCCTTTTGTTTGGGGAACCCCGCTGGGTACAAAGTGGGAAGGGGAgggggggg                                          >  2:257466/1‑137 (MQ=255)                                                                                                                    ggcggtTTTCTGCCATTTATTTTCCCGCCGAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                      <  1:599847/145‑1 (MQ=255)                                                                                                                    ggcggcTTTCTGCCAGCTTTTTTCCCGCCAAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                     <  1:406338/146‑1 (MQ=255)                                                                                                                           gTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGTGCCACA‑G‑GAAAAAAATTAAACACGCCCAGTTGTGTTGGGAGAGCTGCTGGGGAAACTGTGGGGAGGGAGGGGGGGCGGAGCAGATCCAgca                            >  1:117413/1‑146 (MQ=255)                                                                                                                               ccgagtttttttcCCGCCGAAAAAAAC‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt                     <  1:566537/143‑1 (MQ=255)                                                                                                                                       ttttcCCGCCGCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa               <  2:132244/149‑1 (MQ=255)                                                                                                                                         ttcccgccgCAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt            <  2:755470/147‑1 (MQ=255)                                                                                                                                           ccccccgcAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc           <  1:320070/145‑1 (MQ=255)                                                                                                                                            ccgccgAAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg          <  2:407653/149‑1 (MQ=255)                                                                                                                                               ccgcAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAAGG‑G‑AAAAAAAATTTAACCCCCCCTGTTTTGTGGGGAACGCTGCTGGTAAAAAAGTGGGAAGGGAAGGGGGGGGGATCAACTCCCCAACACCGCTAATTTAGTTCGcccc      >  1:313850/1‑148 (MQ=255)                                                                                                                                                   aacaaAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGG‑G‑AAAAAAATTTAAACCCGCCCTGTTGTGTGGGAAACGCCGCTGGGAACAAAGTGGGAAAGGGAGGGGGGGGGATCAGCACCCCAAACGCGCCAATTTAGGTCGCCTCaa    >  2:291814/1‑148 (MQ=255)                                                                                                                                                   aacaaAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATg  <  1:934191/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                         ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAAT‑GCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGA‑G‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357743‑358037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑