Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	42.5%	37.1 / 16.6	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/6);  new base A (0/17);  total (17/23)
Fisher's exact test for biased strand distribution p-value = 1.53e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.64e-01

TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357744‑358028                                                                                                                                                        |                                                                                                                                             tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTTTGTCAGCGGCTCCCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑caac                                                                                                                                              <  1:635146/147‑1 (MQ=255)   aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAcc                                                                                                                                        <  1:864923/151‑1 (MQ=255)          cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTtc                                                                                                                                 >  2:379861/1‑151 (MQ=255)                 ggCATTTCCGGCCGCAGACCGGTGTCAGCGCCTACCGTGATTCTTTC‑CCGCCAACACCCGCGCATTTACCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGGGG‑CGGCTGTCGGCCAGTTTTTTTCCCGCCG‑CAACAAAACCGCCGTTCTCTCCa                                                                                                                           <  2:362128/150‑1 (MQ=18)                   cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCCGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCa                                                                                                                           >  1:569294/1‑148 (MQ=255)                    aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCagt                                                                                                                         >  1:885377/1‑149 (MQ=255)                         cAGCCGCAGCCCTGTGTCAGCGGTTTCCGTTATTCATCC‑CCGCCAACAACCGCGCTTTTACCCACCGCC‑ATGTTAAAAAT‑TGCCTTCGCGG‑CGTCTGTCTGCCAGTTATTTTTCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                   <  2:747615/150‑1 (MQ=255)                         cAGCCGCAGACTTGTGTCAGCGGCTACCGTGATTCATTC‑CCGCCAACACCCGCGCTTTTACCCACCGCC‑ATGTGAAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTCCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                  <  2:37733/151‑1 (MQ=21)                                agcccTGTGTCGGCGCCCCCCTTTATTCTTTC‑CCGCCAACACCCGCGCA‑TTCCCCAACCCCAATGTGAAAAAA‑TCCCTCGGGGG‑CGGTTGCCCCCCAGTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                                            <  1:714513/147‑1 (MQ=255)                                aGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                              >  2:988013/1‑147 (MQ=255)                                     tgtgTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGTGGGGCAAGAGaa                                                                                                       >  2:53587/1‑150 (MQ=255)                                     tgtgTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCggtggg                                                                                                             >  1:731351/1‑140 (MQ=255)                                           aGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGgaaaaaatt                                                                                                >  2:581468/1‑145 (MQ=255)                                              ggCTCCCGT‑ATTCCTTTCCCGCCAACACCCGC‑CCTTTTTCCAACCCC‑CTTTTCAAAAATTGCCTTGGCGG‑GGGCTGTCTGCCCGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCtt                                                                                               <  1:641164/148‑1 (MQ=255)                                                   ccGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGGGAAATaaaattaaaac                                                                                          >  1:618462/1‑139 (MQ=25)                                                    cGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGGAAAA‑ACATTaatac                                                                                         >  2:599423/1‑145 (MQ=25)                                                      tgtttccttc‑cCCCCAACACCCGCGCTTTTACCCACCGCC‑ATGTACAAAAA‑TGCTTTCGCGG‑CGGCTGTCTCCCATTTTTTTTCCCGCCA‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTaa                                                                                            <  1:543440/140‑1 (MQ=255)                                                          tCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGAAAAA‑AATTTAATTCCGTCAtggt                                                                                >  1:709219/1‑149 (MQ=25)                                                             ttt‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAA‑ACTTTaaaaccctccttgttt                                                                              >  1:605001/1‑136 (MQ=25)                                                              ttcccGCCAACACCCGCGCTTTTCACCAACCCC‑ATGAAAAAAAA‑GCCCTGCGCGG‑CGGTTGTCGGCCAGCTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCAt                                                                                   <  1:336153/142‑1 (MQ=255)                                                                    ccAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑AAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAGGAAAA‑AATTTTAGCCCGTCAttgt                                                                                >  1:848553/1‑139 (MQ=25)                                                                      accacccGCGCTTTTACCCAACGCC‑ATGTGAAAAAA‑TGCCTCCGCGG‑CGGCTGTCTCCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAAt                                                                      <  2:93010/145‑1 (MQ=255)                                                                      aacaccCGGGCATTTACCCACCGCA‑TTGTGAAAAAA‑GGCCTGGGGGG‑GGGTTTTCTGCAGGTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                                     <  2:165235/151‑1 (MQ=255)                                                                         acccGCGCTTTTACCCAACGCC‑ATGTGCAAAAA‑GGCCTCCGGGG‑CGGCTGTCTGCCAGCTTTTTTCCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                  <  2:359934/149‑1 (MQ=255)                                                                         acccGCCCATTTACCCACCGCC‑ATGTCAAAAAA‑GCCCTTCGGGG‑CGGTTTTCTGCAAGTTTTTTTCCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                   <  1:447167/148‑1 (MQ=255)                                                                          cccGCTCATTTACCCACCCCC‑ATGTAAAAAAA‑TCCCTCCGGGG‑CGGCTTTCGCCCATTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                   <  1:453650/148‑1 (MQ=255)                                                                                cATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGAGAAAAAAA‑AAATTAAACCCGCCCTTTTTTGTGGGAATCGCTGCTgg                                                             >  2:183414/1‑149 (MQ=37)                                                                                 aTTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCTAAAAAAATAGGCTTAAATCCCgcctgttttgggg                                                                           >  2:234613/1‑123 (MQ=25)                                                                                  tttccccACCGCC‑ATTTCAAAAAT‑TCCCTTCGCGG‑CGGCTGTCTGCCAGTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                               <  1:303669/140‑1 (MQ=255)                                                                                  tttACCCACCCCC‑ATGTGAAAAAA‑TGCCTTCGCGG‑CGGCTTTCTGCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                           <  1:466570/149‑1 (MQ=255)                                                                                         accGCC‑ATGTGCAAAAA‑TGCCTTCGGGG‑CGGCTGTCGGCCAGCTATTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                      <  2:109096/145‑1 (MQ=255)                                                                                                     cAAAAA‑ATCCTTCCCGGCCGGCTGTCTCCCAGCTTTTTTCCCCCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGaa                                         <  2:90568/149‑1 (MQ=255)                                                                                                      aaaaa‑GCCCTCCGCGG‑CGGCTGTCTGCCATTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAg                                        <  1:311494/148‑1 (MQ=255)                                                                                                       aaaa‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAA‑ACTTTTAACCCCCCCCTTTTTGTGGGGATCGCTGGTGGGGAAAAAGTGGGAAAGGGaggggg                                     >  2:934768/1‑146 (MQ=255)                                                                                                       aaaa‑TCCCTCGGCGG‑CGGCT‑TCGCCCCGGTTTTTTTCCCCCGACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGt                                       <  1:56057/148‑1 (MQ=255)                                                                                                                   gggg‑cggcTGTCTGCCAGCTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAg                           <  2:897808/147‑1 (MQ=255)                                                                                                                     gg‑cggtTGTCTCCCGGTTTTTTTCCCGCCG‑AAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGc                          <  2:362257/148‑1 (MQ=255)                                                                                                                                 cccAGTTTTTTTCCCCCCC‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc                  <  1:316523/144‑1 (MQ=255)                                                                                                                                    aGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAGGAAAAA‑AATTTTATACCCGCCTGTTGTGTGGGGATCGCTGCTGGTAAAAAAGG‑GGGAAGGGGAGGGGGGGGGAACAACTCCCGaa                   >  2:269538/1‑141 (MQ=255)                                                                                                                                           tttCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAGAAAAA‑AATTTTAACCCCCCCTTTTTTGTGGGTAACGCTGCTGGGGACAAAGT‑GGGAAAGGAAGGGGGGCGGAACAACCCCCGAAACGCCCCAATTTAGtt   >  2:916364/1‑150 (MQ=255)                                                                                                                                            tcccgccg‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  2:485925/148‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                             TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAA‑TGCCTTCGCGG‑CGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATA‑GCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGT‑GGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357744‑358028

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: ‑