Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	41.7%	48.6 / 25.4	48	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (22/6);  new base A (0/20);  total (22/26)
Fisher's exact test for biased strand distribution p-value = 1.62e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357741‑358032                                                                                                                                                          |                                                                                                                                                 tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                  >  1:537874/1‑150 (MQ=255)  gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                <  1:975266/151‑1 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                                            <  1:1108973/151‑1 (MQ=255)      aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAcc                                                                                                                                            <  2:40892/151‑1 (MQ=255)              gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTtc                                                                                                                                     >  1:160746/1‑150 (MQ=255)                   aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                                >  2:1108333/1‑150 (MQ=255)                      cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                             >  2:426558/1‑150 (MQ=255)                          cccggccccggACTTGTGTCGGCGGCTCCCGGATTTCTTTCCCGCC‑AA‑CACCCGCGCTTTTCCCCACCCCCTTGTCAAAAAATCCCTCC‑GCGCGGGTTGTGTGCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCagta‑g                                                                                                                          <  1:467694/138‑1 (MQ=255)                            cAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCg                                                                                                                     >  2:241991/1‑151 (MQ=255)                             aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCgg                                                                                                                    >  2:994767/1‑151 (MQ=255)                                 gCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCgggggg                                                                                                                >  1:704403/1‑149 (MQ=255)                                    gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCgggg                                                                                                                  >  1:558426/1‑146 (MQ=255)                                    gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGAGCATTTATCCAACGCCATGTGCAAAAATGCCCTC‑CCGCCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCCCCGTTCTCTCCAGTA‑GTGGCgggggtgtg                                                                                                             >  1:348316/1‑146 (MQ=25)                                       cTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCgggggga                                                                                                               >  2:141628/1‑143 (MQ=255)                                       cTGTGTCAGCGACGACCGTGGTTCGTTGCCGCC‑AA‑CAACCCCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCCGACGGCCAGCTAATTTT‑CCGCCGCCACAATACCGCCGTTCCGTCCAGTACGGGGCGGGGCagg                                                                                                              >  1:219591/1‑146 (MQ=18)                                          tgtCGGCGGTTCCCGTGA‑TCCTTTCCCCC‑AACCACCCGCGCTTTTACCCACCCCCTTGTCAAAAAATGCTTCG‑GGGGCGGCTTTATCCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAAt                                                                                                       <  2:1020628/150‑1 (MQ=255)                                            tCAGCGGCTCCCGTGATTCTTTCCCGCC‑AA‑CACCCGCGCTTTTACCCACCGCCATGTGAAAAAATCCCTTC‑GGGGCGCCTGTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAg                                                                                                     <  1:824879/150‑1 (MQ=255)                                            tCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGCAGAG‑aaa                                                                                                        >  2:564101/1‑147 (MQ=255)                                             cggtgggctcccggATTCCTTTCCCCCAAA‑CACCCGCCATTTTACCCAACCCCATGTCAAAAATTCCCTCC‑GCGGGGGTGGTCGGCAGCCTATTTTC‑CGGCCGAAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATa                                                                                                      <  2:942751/136‑1 (MQ=255)                                             cAGCGGCTACCGTATTTCTTTCCCCCC‑AA‑CAACCGCGCTTTTACCCACCGCCATGTGAAAAAATGCCTTC‑GGGGCGGCTGTCTCCCAGCTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATa                                                                                                      <  2:950538/148‑1 (MQ=255)                                               ggggcccccGTGTTTCTTTCCCGCC‑AA‑AACCCGCGCTTTTCCCCACCCCCATGTGAAAAAATCCTTCC‑GGGGCGGTTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCtt                                                                                                  <  2:951662/143‑1 (MQ=255)                                                 ggCTCCCTTGATTCATTCCCCCA‑AC‑CACCCGCGAATTTACCCACCGCCATGTGAAAAAATGCTTCC‑GGGGCGGCGGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTaa                                                                                               <  2:8251/151‑1 (MQ=255)                                                   ctccggttaTTCTTTCCCCCC‑AA‑CACCCGCCCTTTTACCCACCGCCTTGTAAAAAAGGGCTTCC‑GCGGCGGCTGTCTG‑CAGTTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTa                                                                                                <  1:623771/140‑1 (MQ=255)                                                            ttCTTTCCCCCC‑AC‑CACCCGCCCTTTTACCCACCCCAATGTAAAAAAATCCCTCC‑GGGGGGGCTGTCTCCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGt                                                                                         <  1:1051676/146‑1 (MQ=255)                                                                    cGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGGAAAG‑AAAAAAATTTAAAACCCCCATTTTGTggggg                                                                            >  2:679674/1‑150 (MQ=21)                                                                         aa‑caacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGAAGGGAAAAAAACTTTAATCCCG‑CCTGTtgtgt                                                                               >  1:144206/1‑144 (MQ=25)                                                                          a‑caacCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAGACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGCAGGG‑ACAAAAATTTAAAACCGGCCTGTTGTGTgg                                                                             >  1:928635/1‑145 (MQ=25)                                                                               ccccccttttACCCACCGCAATGAAAAAAAATGCCTTC‑GCGGGGCCTGCCTGCAATTTTTTTTC‑CCCCCGCAAAAAATCCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                    <  1:994639/143‑1 (MQ=255)                                                                               ccGCGCTTTTACCCAACCCCATGTGAAAAAATGCCTTC‑GCGGGGGTTGTCGCCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                   <  2:905580/151‑1 (MQ=255)                                                                               ccGCCCATTTACCCACCGCCATGTGAAAAAATGCCTGC‑GCGGCGGTTGCCTCCCGGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                                     <  2:953082/149‑1 (MQ=255)                                                                                cgcgCATTTATCCACCCCCTTGGGAAAAATTGCCTTC‑GCGGGGGCTTTCGCCCACTTATTTTT‑CCCCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                  <  2:202673/151‑1 (MQ=255)                                                                                cgcgCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGCAGCG‑AAAAAACCTTAAGGCCATCCTGTtgtggtgcgaacggctc                                                                   >  2:388699/1‑137 (MQ=25)                                                                                        tATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGAAAAGAAAAAAAATTTAAGCCC‑TCCTGTTTTGTGGGAAACggccgtgggcaca                                                           >  2:558586/1‑138 (MQ=21)                                                                                         aTCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGCAGAG‑AAAAAAATTTAAAACCGTCCCGTTTTGTGGCGAACGCTGCTggggaaaa                                                          >  2:26411/1‑144 (MQ=25)                                                                                         aTCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAGAAAAAAGATTTAAACCCG‑CATGTTTTTTGGCGATCgccggctggt                                                              >  1:719887/1‑138 (MQ=25)                                                                                             acccccATGTGAAAAAATCCCTCC‑GCGGCGGCTGTCGCCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                                       <  1:803109/145‑1 (MQ=255)                                                                                                      gaaaaaaaTTGCTTCGGCGGCGGCTGTCTG‑CAGTTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                              <  1:344288/147‑1 (MQ=255)                                                                                                         aaaaaTCCTTTC‑GCGGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                         <  2:701791/151‑1 (MQ=255)                                                                                                          aaattcccTGC‑GGGGGGGCTGTCTCCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                         <  2:679825/144‑1 (MQ=255)                                                                                                                 cTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCGAGAG‑AAAAAAAATTAAAACCCCCCTCTTTTGTTGGGAACGCTGCTGGTGACAATATGGAAAGGGGAgagggggg                                     >  1:1079207/1‑140 (MQ=255)                                                                                                                      ggggcggcTTTCTCCCATTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                                    <  2:1034331/142‑1 (MQ=255)                                                                                                                              tGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGCAGAG‑AAAAAACTTTAAACCCCTCCTTTTTTGTGGGGAACGCTGCTGGGGAAAAAGTGGGAAGGGGAGGGGGGGGGATCaacccccga                        >  2:497319/1‑140 (MQ=255)                                                                                                                                  tGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGGAGAG‑AAAAAGCTTTAATACCGCCCTGTTGTGTGGGGATCGCTGGTGGGAAAAAAGTGGGAAGGGGAGGGGGGGGGATCAGATcc                           >  2:817818/1‑141 (MQ=255)                                                                                                                                    ccAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc                     <  1:504636/145‑1 (MQ=255)                                                                                                                                            tttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt        <  2:464002/150‑1 (MQ=255)                                                                                                                                            tttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt        <  2:151620/150‑1 (MQ=255)                                                                                                                                               t‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg     <  2:190351/150‑1 (MQ=255)                                                                                                                                                cccgccaAAAAAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc      <  1:111025/148‑1 (MQ=255)                                                                                                                                                  cgccgcAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGGCAGAG‑AAAAAAATTTTAATCCCCCATGTTTTGTGGGGAACGCTGCTGGGGACAAAGTGGGAAGGGGAGGGGGGCGGAACAACCCCCAAAACGCGCCAAATTAGtttccc   >  2:928111/1‑146 (MQ=255)                                                                                                                                                  cgccccAAAAAAGCCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt  <  2:131645/151‑1 (MQ=255)                                                                                                                                                          |                                                                                                                                                 TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCC‑AA‑CAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTC‑GCGGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTA‑GTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357741‑358032

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: ‑