Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	43.6%	35.1 / 20.6	39	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (18/4);  new base A (0/17);  total (18/21)
Fisher's exact test for biased strand distribution p-value = 1.81e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.61e-01

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGA  >  NC_000913/357742‑358038                                                                                                                                                        |                                                                                                                                                       gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa                                                                                                                                                      <  2:1043253/151‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACaaaa                                                                                                                                                    <  2:201795/150‑1 (MQ=255)                 cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTcc                                                                                                                                      >  1:1247327/1‑151 (MQ=255)                       aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCagtagt                                                                                                                                >  1:684613/1‑151 (MQ=255)                         tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                              >  1:301029/1‑151 (MQ=255)                          ccAGCCGCAGATTTGTGCCGGCGTCTACCGTATTTCATTCCCCCAAACACCCGCGCTTTTCCCAAACGCATTTTAAAAAAATGCCTT‑G‑GGGGCGGCTGTCTCCCATTTTTTTTCCCGCCGC‑AAAAAAGCCGCCGTTCTCTCCAGTAGTg                                                                                                                               <  1:1299140/149‑1 (MQ=255)                            aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                             >  2:333439/1‑149 (MQ=255)                            aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                           >  2:992102/1‑151 (MQ=255)                              ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                         >  1:343541/1‑151 (MQ=255)                              ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                         >  1:546340/1‑151 (MQ=255)                                gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                         >  2:307331/1‑149 (MQ=255)                                  aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGcg                                                                                                                       >  1:469554/1‑148 (MQ=255)                                   gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggg                                                                                                                      >  2:1182063/1‑146 (MQ=255)                                     ccTGTGCCAGCGCCTCCCGTGTTTTATTCCCCCCAACACCCCCCCTTTTACCCACCGCCTTGTGAAAAAAGCCCTC‑G‑GCGGGGGTTGTC‑GCCCCCTTTTTTTCCCCCCCAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                                    <  1:1360619/149‑1 (MQ=255)                                      cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCacggga                                                                                                                  >  1:275227/1‑145 (MQ=255)                                           tCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCACTCCAGTAGTGGCGGGGCgaaagaaaaa                                                                                                              >  1:755369/1‑147 (MQ=255)                                                gcctcccGTTATTCTTTCCCGCCACCACCCCCGCATTTCCCCAACCCCATTTCAAAAAATGCTTG‑C‑GGGGGGGTTGTCGGCCGGTTTTTTTCCCCCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                                   <  1:1230959/134‑1 (MQ=255)                                                           ttCTTTCCCCCCAACACCCGCGCTTTTACCCACCCCCATGTAAAAAATTCCCTC‑G‑GCGGGGGTTGTCGCCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                                               <  1:1207428/148‑1 (MQ=255)                                                                     ccaccaCCCGCGTTTTTACCCACCGCATTGTAAAAAACTCCCTC‑C‑GGGGGGGTTTTCTGCCATTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                                    <  2:387154/149‑1 (MQ=255)                                                                       aacaccCGCGCTTTTCTCCAGCGCCATGT‑AAAAAATTCCTTCC‑GGGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                                <  1:915723/151‑1 (MQ=255)                                                                            ccccgcTTTTACCCAACGCCATGTAAAAAAATCCCTC‑C‑GCGGGGGCTGTCTGCCAGTTTTTTTCCCGCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                            <  1:19443/147‑1 (MQ=255)                                                                                    ttACCCACCCCCTTGTGAAAAAAGGCTTC‑C‑GCGGCGGCTGTCTGCAAGTTTTTTTCCCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAAc                                                                   <  1:1267159/150‑1 (MQ=255)                                                                                      aTCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAGATTTTAAACCGCCCTTTTTTGTGGGGATCGCtggt‑ggggaaaa                                                                 >  1:1123134/1‑144 (MQ=25)                                                                                       cccacccctaTGTGAAAAAATGCTTC‑C‑GGGGCGGCTTTCTGCCAGTTATTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACa                                                                  <  1:94794/139‑1 (MQ=255)                                                                                        ccacccccATGTGAAAAAATCCCTC‑C‑GGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAt                                                                <  1:538392/143‑1 (MQ=255)                                                                                            ccccATGTAAAAAAATCCTTC‑C‑GCGGCGGCTTTCTCCCAGTTTTTTTCCCGCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAt                                                                <  1:1305860/143‑1 (MQ=255)                                                                                                     cAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAATCCCTCCTTTTTTGTGGGGATTGCTGCC‑GGTAACAAAGTGGGAAAGGGAAgg                                                 >  1:1374053/1‑150 (MQ=255)                                                                                                      aaaaaTGCCCT‑CGGCGGCGGTTTTCTGCCAGTTTTTTTCCCGCCCA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTg                                                <  2:979820/151‑1 (MQ=255)                                                                                                           tGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAAATTTTAAACCGTCCTGTTGTGTGGGAATCGGTGCT‑GGGGAAAATTT‑GGGAAGGGGAggggggggg                                          >  1:613081/1‑143 (MQ=255)                                                                                                                  c‑gcgGCGGCCTCCTGCAACATTTTTTCCCGCCGA‑AAAAGATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGTT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAgt                                    <  2:337998/151‑2 (MQ=255)                                                                                                                      ggggtttgtcgcccAGTTTTTTTCCCCCCGC‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCt                                   <  1:957324/137‑1 (MQ=255)                                                                                                                      gggggttGTCGGCCAGTTTTTTTCCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAAt                                        <  2:161177/138‑1 (MQ=255)                                                                                                                      ggcggcTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGGGAAAAAAAATTAAAACCGCCCTGTTTTGTGGGGATAGCGGGTGGGTAAAAATTG‑GGAAGGGGAAGGGGGGGGaacagaccc                                  >  2:169498/1‑144 (MQ=255)                                                                                                                      ggcggcTGCTTCCCATTTTTTTCTCCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAAt                                        <  1:508892/144‑1 (MQ=255)                                                                                                                                  ccgtttttttgcccgccaA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                       <  2:44358/137‑1 (MQ=255)                                                                                                                                  ccattttttttcCCGCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc                       <  2:586969/142‑1 (MQ=255)                                                                                                                                  ccAGCTTTTTTCCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg                        <  1:883383/148‑1 (MQ=255)                                                                                                                                  ccAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAACCCCCCCTGTTTTGTGGGGATCGCTGCT‑GGGTAAAAAAT‑GGGAAGGGGAGGGGGGGGGATCAGCCCCCCAACCgcgccc                     >  1:1106785/1‑149 (MQ=255)                                                                                                                                         tttttCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAGCTTTTAAACCCCCCTGTTTTGTGGGGATTGCTGCT‑GGGAGAAAAAT‑GGGAAGGGGAAAGGGGGGGATCAACCCCAGAAACgcgcccatt                  >  1:215033/1‑142 (MQ=255)                                                                                                                                            tcccccccc‑aaaaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc            <  1:641714/142‑1 (MQ=255)                                                                                                                                             cccgccgA‑AAAAACGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGc          <  2:60276/150‑1 (MQ=255)                                                                                                                                                  cctaaacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa      <  1:333447/147‑1 (MQ=255)                                                                                                                                                      aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGa  <  2:1202200/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                       GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTT‑C‑GCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATGA  >  NC_000913/357742‑358038

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑