Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	57.7%	11.2 / 31.2	26	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (9/2);  new base C (0/15);  total (9/17)
Fisher's exact test for biased strand distribution p-value = 1.76e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.78e-05

CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357731‑358015                                                                                                                                                          |                                                                                                                                          cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                          >  1:284820/1‑151 (MQ=255)    gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                       <  1:238261/151‑1 (MQ=255)          cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaac                                                                                                                                 >  2:30893/1‑151 (MQ=255)              tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                              >  1:67965/1‑150 (MQ=255)                       cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑G‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgccg                                                                                                                      <  2:255887/148‑1 (MQ=255)                               gCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagt                                                                                                           >  2:37167/1‑151 (MQ=255)                                cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagt                                                                                                           >  2:197865/1‑150 (MQ=255)                                   tcccAGCCGCAGCCTTGTGTCAGGGGCTCCCGTGTTTCTTTCCCCCCAACACCCGCGCTTTTAC‑CAACCGCCTTGTGAAAAAATGC‑TTC‑C‑GCGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCagtagt                                                                                                        <  2:124397/148‑1 (MQ=255)                                            cagccttgtgtgGGCGGTTCCCGTTTTTCTTTCCCCCCAACACCCGCCCTTTTAC‑CCACCCCCGTGTAAAAAATTCC‑CTT‑C‑GCGGCGCCTGCCGCCCGGCTTTTTTCCCGCCGAAACAAAA‑CCGCCGTTCTCTCCAGTAGTgg                                                                                                      <  1:428036/137‑1 (MQ=255)                                             aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                >  2:396836/1‑147 (MQ=255)                                             aGACCTGTGTCAGCGGCTACCGAGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑A‑GCGGCGGCTGTCTGCCAGCTATTTTTACGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTCGCgggggc                                                                                               >  1:598196/1‑147 (MQ=255)                                                  tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGcgaaaa                                                                                           >  2:613362/1‑143 (MQ=255)                                                    tgccgggggCTCCGGTGATCCATTCCCCCCAACACCCGCGCTTTTAC‑CCAACGCAATGTG‑AAAAATGCTCTC‑G‑GGGGGGGCTTTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                               <  1:417383/135‑1 (MQ=255)                                                     gtCGGCGTCTCCCTTCATTCTTTCCCCCCAACAGCCCCTATTTTAT‑CCACCCCCATGTGAAAAATGGC‑TTT‑G‑GCGGGGTCTGTTGCCCACCTATTTTCCCGCCGAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaaa                                                                                        <  1:457894/148‑1 (MQ=255)                                                         ggcgaccccGTGTTTCATTCCCCCCAA‑AACCCCGCCTTTTTACCAACCCCGTTTGCAAAAATGC‑CTTCC‑GGGGGGGTTGTC‑GCCAGGTTTTTTCCCCCCCAAAAAAAACCCGCCGTTCTC‑CCAGTAGTGGCGGGGCAAGAGAAATa                                                                                      <  1:297578/139‑1 (MQ=255)                                                         gcgcccaCCGTGTTTCTTCCCCCCCACCACCCGCCCTTTTAC‑CCACCCCAATGCAAAAAAATCC‑CTT‑G‑GGGGCGGTTGTCGCCCACATATTTTCCCGCCAAAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                 <  1:197888/145‑1 (MQ=255)                                                                 cgttttcctttcccGCCAACAACCCCGCATTTCC‑CCACCGCCATTTAAAAAAACGC‑CTC‑C‑GCGGCGGCTGTTGCCCAGCTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCttt                                                                                 <  2:430524/131‑1 (MQ=255)                                                                             cccccAACACCCGCATATTTAC‑CAAACGCCGTGTAAAAAATTGC‑CTC‑C‑GGGGGGGCGTTCTGCCAGTTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                               <  1:600227/146‑1 (MQ=255)                                                                                    cacccGCGCTTTTCC‑CCACCGCAATGTGAAAAATTCC‑TTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                        <  2:372424/146‑1 (MQ=255)                                                                                              ttttccccacccccttgtaCAAAAATCC‑TTG‑C‑GGGGCGGTTGTCTCCCGGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                              <  1:445186/135‑1 (MQ=255)                                                                                                        cGCCATG‑GAAAAAAAGC‑CCT‑CGGGGGGGGCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                          <  1:647701/144‑1 (MQ=255)                                                                                                               gtgaaaaaaGC‑CTTCC‑GCGGCGGCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGAGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                        <  1:520963/137‑1 (MQ=255)                                                                                                                   aaaaTGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAACCCCCCCTGTTTTGTGGGGAACGCTGCTGGGGAAAAAGAGGAGAAGGGAAgggg                        >  2:601853/1‑148 (MQ=255)                                                                                                                                cggggcggcTGTCTGCCATCTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCa               <  2:655303/146‑1 (MQ=255)                                                                                                                                              cccAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc  <  2:665120/147‑1 (MQ=255)                                                                                                                                                cggCTTTTTTCCCCCCACAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAAcc    <  1:612055/142‑1 (MQ=255)                                                                                                                                                 ggtttttttcCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGa       <  1:345561/135‑1 (MQ=255)                                                                                                                                                          |                                                                                                                                          CTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTAT‑CCAACGCCATGTGCAAAAATGC‑CTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGA‑AAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357731‑358015

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 25 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑