Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	56.7%	1.2 / 35.4	30	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (10/3);  new base A (0/17);  total (10/20)
Fisher's exact test for biased strand distribution p-value = 9.52e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.07e-05

ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357743‑358026                                                                                                                                                         |                                                                                                                                          aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGcaacaa                                                                                                                                         >  1:120112/1‑150 (MQ=255)    aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAGCCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                     <  1:409656/151‑1 (MQ=255)     gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAAccg                                                                                                                                    <  2:417174/151‑1 (MQ=255)      cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACaaaa                                                                                                                                       <  1:851654/147‑1 (MQ=255)           cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                              >  2:302671/1‑151 (MQ=255)           cgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                              >  2:545762/1‑151 (MQ=255)             cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctc                                                                                                                            >  2:336706/1‑151 (MQ=255)               tCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtctctc                                                                                                                          >  1:148393/1‑151 (MQ=255)                          cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                               >  2:760498/1‑151 (MQ=255)                            gCCGCAGACATGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCACGCATTTAT‑CCAC‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTTTCTG‑CCAGCTATTTTTCCGCCGCAACAAAAACGCCGGTCTGTCCAGAAGTGGCggg                                                                                                             >  1:157515/1‑151 (MQ=21)                             cggcatgccgttatCAGCGCCTCCCGAGTTTCTTTCCCCCC‑ACCACCCGCTCATTCCA‑CCAC‑CCCAATGTAAAAAAAGCCTTTC‑GGGGCGTCTGTCCG‑CCAGCTATTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                <  2:233424/134‑1 (MQ=255)                             ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                            >  1:193516/1‑151 (MQ=255)                             ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                              >  1:1069728/1‑149 (MQ=255)                                    ccTTTGTGAGCGGCTCCCGTTATTCTTCCCCCCC‑ACCACCCGCG‑TTTTAA‑CCCA‑CCTCATTGTAAAAAATGCCCTCGGCGGCGCCTGTCTC‑CCGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                                        <  1:1164921/148‑1 (MQ=255)                                       gttccAGCGGCTCCCGTATTTCTTTCCCCCC‑AAC‑‑CCCCGCATTTTTCCCAACCCCCATGTGAAAAACTCCCTCC‑GCGGCGGCTGTCAC‑CCGTTTTTTTCCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                          <  1:121597/139‑1 (MQ=255)                                         gtCGGCGGCCCCCGTG‑TTTATTTCCCCCAAACACCCGCGATTTTAC‑CCAC‑CCCAATGT‑AAAAAATTCCTTCGGCGGCGGCTTTCTG‑CCAGTTTTTTTCCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                                      <  2:387956/145‑1 (MQ=255)                                                    ccgaaaTTCTTTCCCGCC‑AACACCCGCGCTTTTAC‑CCAC‑CCCCATGTGAAAAAATGCCTCC‑GCGGCGCCTGTCTC‑CCAGTTATTTTGCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                          <  2:78185/141‑1 (MQ=255)                                                    ccGTTATTCGTCTCCCCA‑AACACCCACTCATTTAC‑CCAC‑CGCATTGTGCAAAATCGCCCTC‑GGGGCGCCTTCCTC‑CCAGCTATTTTCCCGCGGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTaa                                                                                          <  2:1082141/146‑1 (MQ=255)                                                     cGTGATTCTTTCCCGCA‑AACACCCGCGCTTTTCC‑CCAC‑CGCCATGTGAAAAATTCCCTCC‑GCGGCGGCTTTCCC‑CCAGCTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGc                                                                                        <  2:236693/147‑1 (MQ=255)                                                                 ccccc‑AACACCCGC‑CAATTAC‑CCAA‑CGCCCTGGTGAAAAATTCCTTCGGCGGGGGTGTTCTC‑CCAGTTTTTTTCCCGCCGCAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                        <  1:792937/148‑1 (MQ=255)                                                                 ccGCC‑ACCAACCGCACTTTCAC‑CCAC‑CCCTATTTCAAAAATTGCCTCC‑GCGGCGGCTGTCTC‑CCAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtg                                                                           <  2:1231685/148‑1 (MQ=255)                                                                     c‑aacaaCCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAATTTaaaaacgccccttt                                                                              >  1:58187/1‑129 (MQ=25)                                                                            ccGCGCTTTTAC‑CCAC‑CGCCATGTGAAAAAAGACCTCG‑GCGGCGGGTGTCCG‑CCGGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                               <  2:71137/150‑1 (MQ=255)                                                                                          caaccccatggtaaaaaaaTGCCTCG‑GCGG‑GGCTTTCCCCCCAGTTTTTTTCCCGCAGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtgt                                                 <  1:844248/137‑1 (MQ=255)                                                                                            accccaggggcaaaaaaTCCTTCC‑GCGGGGGTTGTCTG‑CCAGTTTTTTTCCCCCAAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAAtg                                                  <  1:383507/136‑1 (MQ=255)                                                                                                                          gccTGTCTC‑CAAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                   <  2:1112734/148‑1 (MQ=255)                                                                                                                               tCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTTAACACGCCATGTTTTGTTGGGATCGCTGGTGGGTAACAA‑ATGGTGAGGGGAGGGGGGGGGATAAGCTCCCGAAAcgc             >  2:652821/1‑151 (MQ=255)                                                                                                                                   cccggtttttttcCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                            <  1:47860/125‑1 (MQ=255)                                                                                                                                    ccAGTTTTTTTCCCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa         <  2:1096192/151‑1 (MQ=255)                                                                                                                                      actttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                 <  2:653609/136‑1 (MQ=255)                                                                                                                                            tttcCCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt  <  1:1120855/150‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                          ATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AACAACCGCGCATTTAT‑CCAA‑CGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTG‑CCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGT  >  NC_000913/357743‑358026

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: ‑