Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	51.3%	25.2 / 61.6	39	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/4);  new base A (0/20);  total (15/24)
Fisher's exact test for biased strand distribution p-value = 1.54e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.51e-06

AGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357746‑358037                                                                                                                                                     |                                                                                                                                                     aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCTTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAAcc                                                                                                                                                <  2:728787/151‑1 (MQ=255)  gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAAcc                                                                                                                                                <  2:786506/150‑1 (MQ=255)           aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTtctct                                                                                                                                      >  1:17788/1‑151 (MQ=255)           aTCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTtctct                                                                                                                                      >  1:476869/1‑151 (MQ=255)             cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTtctct                                                                                                                                      >  2:734458/1‑149 (MQ=255)                  attcccAGCCGCAGCCCTGTGTCAGCGGCTCCCGTGATTCTTTTCCGCCAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTTTCTGCCAGTTTTTTT‑C‑CC‑GCCGCAAAAAAACCGCCGTTCTCTCCagtag                                                                                                                               <  1:181352/147‑1 (MQ=21)                         gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                        >  1:430604/1‑151 (MQ=255)                          ccccAGACCTTTTTCCGCGCCTACCGTGATTCATTTCCCCCAACCCCCGCGCATTTTTCCAACGCCTGGTGCAAAAATCCCTTCCC‑GGGGTCTGTCGTCCAGCTTTTTT‑C‑CC‑GCCGCAACAAAACCGCCGTtc                                                                                                                                         <  2:815484/130‑1 (MQ=255)                             cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggtg                                                                                                                       >  1:678193/1‑146 (MQ=255)                             cAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                        >  2:984825/1‑147 (MQ=255)                              aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggg                                                                                                                      >  2:832828/1‑147 (MQ=255)                                cccTGTGCCAGCGGCTCCGTTTTTTCTTTCCCGCAAACACCCGCCGATTTACCCAACCCCATGCACAAAATGCCCTCCGG‑GGCGGCTGTCTGCCAGTTTTTTT‑C‑CC‑GCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                                  <  2:508847/149‑1 (MQ=255)                                aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggga                                                                                                                    >  1:309704/1‑145 (MQ=255)                                 cttgtgTCGGCGGCTCCCGTATTTCATTCCCGCCAACACCCGCGCTTTTATCCACCCCCATGTGAAAAAATCCCTTCGC‑GGCGGCTGTCTGCCAGTTTTTTT‑C‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                                   <  1:585679/146‑1 (MQ=255)                                 ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                        >  2:834207/1‑143 (MQ=255)                                   tgtgTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggggggagggaa                                                                                                               >  2:959260/1‑142 (MQ=255)                                   tgtgCCGGCGGCTACCGTATTTCTTTCCCCCCAAAACCCGCGCTTTTACCCAACCCATTGTGAAAAAAGGCTTCCGG‑GGCGGCTGTCTGCCAGTTTTTTT‑C‑CC‑GCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAaga                                                                                                                  <  1:263130/147‑1 (MQ=255)                                                  ctggATCCATTCCCGCCAACCCCCGCTCATTTCCCCAACCCCGTGTAAAAAAATGCTTTCGG‑GGCGGCTTTCTGCCAGTTTTTTT‑C‑CC‑GCCGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTa                                                                                                     <  2:890070/141‑1 (MQ=255)                                                           ttcccGCAAAAACCCGCGCTTTTACCCACCGCAATGTGAAAAAATGCCTCCGC‑GGGGGTTGTCTGCAAGTTTTTTT‑T‑CC‑GCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgttg                                                                                       <  1:34897/146‑1 (MQ=255)                                                             cccccaaacaccCGCGCTTTTACCCAACCCAATGTGAAAAAATGCTTCCGC‑GGCGGCTGTCGGCCAGTTTTTTT‑C‑CC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTtgtg                                                                                     <  1:841971/143‑1 (MQ=255)                                                              ccGCAAACACCCGCGCATTTACCCAGCCCCTTGTAAAAAACTGCCTTCGG‑GGGGGCGTTCCGCCAGCTTTTTT‑C‑CC‑GCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgttgt                                                                                      <  1:529052/147‑1 (MQ=255)                                                                   aacaccCGCGCATTTATCCAACCCCAGGTGCAAAAATGCCTTCGG‑GGGGGCTGTCTGCCAGCTTTTTT‑C‑CC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGc                                                                                 <  1:218647/147‑1 (MQ=255)                                                                        ccGCGCTTTTCTCC‑ACCCCATGGAAAAAAAGTGCTTCGCGGGCGGCTGTC‑CCCAACTTTTTT‑TCCC‑GCAAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                          <  2:560931/149‑1 (MQ=255)                                                                           cgcATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GGAAAAAATTTTAACCCCTCCTGTTGTGTGGGAGTCGCTGCTgg                                                                     >  1:69191/1‑151 (MQ=25)                                                                                     cAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAA‑GAAAAAAATTTTAACCCCCCCTGTTTTGTGGGGAACGCTGCTGGGGACaa                                                               >  1:156832/1‑147 (MQ=25)                                                                                                                 ggcggtTGCCTGCCATATTTTTT‑G‑CC‑GCAAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                                 <  2:971473/150‑1 (MQ=255)                                                                                                                 ggcggcTGTCTGCAGGTTTTTTT‑C‑CC‑GCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                     <  1:834432/146‑1 (MQ=255)                                                                                                                 ggcggcTGTC‑GCCAATTTTTTTCT‑CC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc                                   <  1:485496/148‑1 (MQ=255)                                                                                                                 ggcggcGGTCTCCCAGTTTTTTT‑C‑CC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                     <  1:593768/146‑1 (MQ=255)                                                                                                                  gcggcTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGGAAAAAATTTTAAACCCCCCCAGTT‑TGTGGGAAACGCTGCTGGGGAAAAAATGGGAAGGGGAGTGGGGGGGAACAACTcc                                >  1:778456/1‑150 (MQ=255)                                                                                                                    ggcTGTCTGCCAGTTATTTT‑C‑CC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                               <  1:835601/149‑1 (MQ=255)                                                                                                                         tcggCCAGTTTTTTT‑C‑CC‑GCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                               <  2:464625/141‑1 (MQ=255)                                                                                                                          cTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAAATTTTAAACCCCCCTGTTGTGGGGGAAACGCTGCTGGGTAAAAAATGGGAAGGGGAGGGGGGGGGAACAGCTCCAGaaac                          >  1:641567/1‑146 (MQ=255)                                                                                                                              ccgacttttt‑t‑CCGGCCGAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt                     <  1:662013/144‑1 (MQ=255)                                                                                                                               agttttttt‑c‑CC‑GCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                          <  1:512148/138‑1 (MQ=255)                                                                                                                                  tttttt‑c‑CC‑GCCACAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAGcc                          <  2:91566/138‑1 (MQ=255)                                                                                                                                    tttt‑c‑CC‑CCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAAt                  <  1:394549/146‑1 (MQ=255)                                                                                                                                     ttt‑c‑CC‑GCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt             <  1:44932/150‑1 (MQ=255)                                                                                                                                                 gcAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGA‑GAAAAAACTTTTAGCCCGGCCTTTTGTTTGGGAATCGCTGGTGGTGAAAAAGTGGGAAGGGGAGGGGGGGGGGACAGCCCCAAAACCGCGCCAATTGaagttgccccca    >  1:410044/1‑139 (MQ=255)                                                                                                                                                   aacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATg  <  2:960156/150‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                     AGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGC‑GGCGGCTGTCTGCCAGCTATTTT‑T‑CC‑GCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAATG  >  NC_000913/357746‑358037

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑