Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	60.5%	‑0.4 / 29.4	39	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (9/6);  new base A (0/23);  total (9/30)
Fisher's exact test for biased strand distribution p-value = 3.07e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.87e-02

TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357741‑358035                                                                                                                                                            |                                                                                                                                                     tGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaac                                                                                                                                                      >  1:990337/1‑150 (MQ=255)   aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                                                    >  1:495037/1‑150 (MQ=255)         gttgcgcTTCAGCCAATTCAAGCCGCAGCCCTGTGTCAGCGGCTACCGTACTTAATTT‑CCGCCAAAAACCGGGCTTTTATCCAACGCC‑ATGTGCAAAAAGGCCTT‑C‑GC‑GGCGGTTGTCTGCCAGCTATTTTA‑CCGCCGCAAGAAAAccgcc                                                                                                                                             <  2:978285/148‑1 (MQ=18)           aGCCCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGGGATTCATTC‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGGGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCGGCTATTTTT‑CCGCCGCAACAAAAccgcc                                                                                                                                             <  2:605195/149‑1 (MQ=255)                 ccggccattccccgCCCCAGCCCTGGTTCAGCGCCTGCCGTGATTCTTCC‑CCCCCACCACCCGCGCTTTCATCCACCGCC‑TTGGGCAAAAATCCCTT‑C‑GC‑GGCGGCTGTCTGCCGGCTTTTTTC‑CCGCCGCAACAAAACCGCCGTtctctc                                                                                                                                     <  2:113128/138‑1 (MQ=255)                      cAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                                                 >  2:253838/1‑150 (MQ=255)                       aaTTCCAGCCGCAGACCTGTGTCAGGGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTC‑C‑TC‑GGCGGCGGTCTGCCAGCTATCTTT‑CCGACTCCACAAAAcccacgcgctaccc                                                                                                                                    >  2:532583/1‑134 (MQ=17)                          tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAAACGCCGTTCTCTCCAGTAGTgg                                                                                                                            >  1:621988/1‑151 (MQ=255)                            cacccGCAGCCTTGTGTGAGGGCCTACGGTAATTCATCC‑CCCCCAACACCCGCGCTTTTTCCCACCGCC‑TTGTGAAAAATTCCTTT‑C‑GC‑GGCGGTTGTCGGCCGGTTTTTTTC‑CGGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGc                                                                                                                           <  2:730909/147‑1 (MQ=255)                               ccGCAGCCTTGTGTCAGCGGCTCCCGTGTTTCTTTC‑CCCCCAACACCCGCCCATTTACCCAACCCC‑TTGTGAAAAAATCCTTC‑C‑GC‑GGCGGCTTTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                         <  1:339502/149‑1 (MQ=255)                                cgcggccttgtgTCAGCGGCTCCCGTGTTTCATTC‑CCCCCAACAACCGCGCTTTTCCCCAGCGCC‑ATGTAAAAAAATCCCTC‑C‑GG‑GGCGGCTGCCTCCCAGTTATTTTT‑CCGCCCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                        <  1:280781/141‑1 (MQ=255)                                     cccTGTGTCAGGGGCTCCCGTTTTTCATTC‑CCCCCAACACCCGCGCATTTACCCACCGCC‑ATGTGAAAAAATGCTTT‑C‑GG‑GGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAag‑ag                                                                                                                <  1:53541/150‑1 (MQ=255)                                       cTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGctgga                                                                                                                  >  2:548655/1‑144 (MQ=255)                                        tgtgTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AG‑aa                                                                                                             >  1:808153/1‑150 (MQ=255)                                          tgtCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggcgggag                                                                                                                >  2:890196/1‑140 (MQ=255)                                           gtaaggggCTCCCGT‑ATTTATTTCCCCCCAAAACCCGCGCTTTTA‑CCAACCCCAATGT‑CAAAAATGCCTTCC‑GC‑GCCGGCTGTCT‑CCCGCTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑aaa                                                                                                            <  1:254449/142‑1 (MQ=255)                                                cGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGAGGTAG‑AG‑aaaaaagatt                                                                                                     >  1:152580/1‑143 (MQ=25)                                                 ggCTCCCGTGATTATTTC‑CCCCCAACACCCGCGCTTTTACCAAACGCA‑ATGTGAAAAAATGCTTT‑C‑GC‑GGCGGCTTTCGGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTa                                                                                                    <  1:876614/150‑1 (MQ=255)                                                        gtgtTTCTTTC‑CCGCCAACACCCGCGCTTTTACCCACCGCC‑ATGTGAAAAAATGCCTT‑C‑GG‑GGCGGCTGTCTCCCAGCTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAg                                                                                                  <  1:487485/145‑1 (MQ=255)                                                        gTGATTCATTC‑CCGCCAACACCCGCGCTTTTACCCAACGCC‑ATGTGAAAAAATGCTTC‑C‑GG‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGt                                                                                             <  1:284559/150‑1 (MQ=255)                                                                    ccgaccacccccGCGCACTTCTCCACCGCC‑TTGTCCAAAACTGCCTG‑C‑GG‑GGGGCTTGTCGCCGAGTTGTTTTC‑CCCCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTgg                                                                                 <  2:539611/141‑1 (MQ=255)                                                                    cccccAACACCCGCGCTTTTACCCACCCCC‑TGGTAAAAAAATGCCTC‑C‑GG‑GGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTtgtgt                                                                                   <  1:890944/146‑1 (MQ=255)                                                                    ccGCCACCACCCGCGCATTTACCCACCCCC‑ATGTGAAAAAATGCCTC‑C‑GC‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTtgtg                                                                                    <  1:147574/148‑1 (MQ=255)                                                                       ccAACACCCGCGCATTTATCCACCGCC‑ATGTACAAAAATCCCTT‑C‑GC‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                                              <  1:300337/151‑1 (MQ=255)                                                                       caaacaccCGCGCTTTTACCCAACGCC‑ATGTGAAAAAAGGCTTC‑C‑GC‑GGCGGCTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                               <  1:984024/148‑1 (MQ=255)                                                                         aacaccCGCGCTTTTCCCCAGCGCC‑ATGTACAAAAAGGCCTG‑C‑GG‑GGGGGCTGTCGGCCGGCTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCa                                                                               <  2:54120/148‑1 (MQ=255)                                                                            acccGCGCATTTATCCACCGCC‑TTGTGAAAAAATGCCTC‑C‑GC‑GGCGGCTGTCTGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgc                                                                          <  1:220189/148‑1 (MQ=255)                                                                              ccccgatttgaTCCACGGCC‑GTGAGAAAAAAGGCC‑T‑C‑GCGGGCGGTTGTCACCGAGTTTTTTTC‑CCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                        <  2:571721/140‑1 (MQ=255)                                                                                       gaTCCCACCCC‑ATTGGGAAAAATTCCCT‑CGGC‑GGCGGCGTTCTCCCGGCTTTTTCC‑CCGCCGAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTa                                                                  <  2:839285/147‑1 (MQ=255)                                                                                        aTCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AGAAAAAAAATTTAATCCC‑TCATGTTTTGTGGGGATAGCTGCTggggaaaa                                                              >  1:86467/1‑144 (MQ=25)                                                                                         cccACCGCC‑GTGTGAAAAAAGGCTTT‑G‑GG‑GGCGGCTGTCTGCCAGTTATTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAtg                                                           <  1:230875/150‑1 (MQ=255)                                                                                            accGCC‑ATGTCAAAAAATCCCTC‑C‑GC‑GGCGGCTGTCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAtg                                                           <  1:946600/146‑1 (MQ=255)                                                                                            aaCGCC‑ATGGGAAAAAATGCCTC‑C‑GC‑GGCGGCTGTCTGCCGTTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAtgtg                                                         <  1:845435/150‑1 (MQ=255)                                                                                                 cattgtaaaaaaaTGCCTC‑C‑GC‑GGGGGCTGTCTCCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAg                                                    <  1:956107/143‑1 (MQ=255)                                                                                                         aaaaaTGCCTC‑C‑GC‑GGCGGCTTTCTGCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTgc                                            <  1:298847/151‑1 (MQ=255)                                                                                                           aaaTGCCTC‑G‑GG‑GGCGGCTTTCTTCCAGTTATTTCC‑CCGCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTgcgg                                          <  2:928119/151‑1 (MQ=255)                                                                                                            aaaaaggcttcgggggcggtGGTCTCCCAGTTTTTTTC‑CCCCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGaa                                                <  1:282545/133‑1 (MQ=255)                                                                                                                             ggcTCTCTCCAAGCTTTTTTT‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCa                                   <  2:385901/143‑1 (MQ=255)                                                                                                                                   cTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAG‑AG‑AAAAAAATTTTAAACCCCCATGTTTTTTGGGGATAGCCGCTGGGGAA‑AAATTGGGAAGGGGAGGGGGGGGGATCAACTCCCGaa                          >  1:891325/1‑146 (MQ=255)                                                                                                                                           ttttttc‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg              <  1:186668/148‑1 (MQ=255)                                                                                                                                                ttcccgccaCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGtt          <  2:860393/147‑1 (MQ=255)                                                                                                                                                         caacaaAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAAG‑AAAAAATTTTAAACCCG‑CATGTTTTTTGGGAATCGCCGCTGGGGACAAATTGGGAAAGGGGAGGGGGGGGAA‑CAACTCCACAACCGCGCCAATTTAGTTTGccccca  >  1:531966/1‑145 (MQ=255)                                                                                                                                                            |                                                                                                                                                     TGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCC‑ATGTGCAAAAATGCCTT‑C‑GC‑GGCGGCTGTCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAG‑AG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCAA  >  NC_000913/357741‑358035

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑