Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	46.9%	43.9 / 25.8	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (17/9);  new base A (0/23);  total (17/32)
Fisher's exact test for biased strand distribution p-value = 4.96e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.65e-01

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357742‑358032                                                                                                                                                       |                                                                                                                                               gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑caaca                                                                                                                                               >  2:863086/1‑150 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑caaca                                                                                                                                               <  1:789699/150‑1 (MQ=255)  aTAAGCGTATCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCTGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGGCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaa                                                                                                                                             <  1:707833/151‑1 (MQ=255)  aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaa                                                                                                                                             <  1:269213/151‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaaa                                                                                                                                            <  2:7580/150‑1 (MQ=255)    aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAc                                                                                                                                           <  1:28940/151‑1 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAccg                                                                                                                                         >  1:232624/1‑151 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAccg                                                                                                                                         <  1:658013/151‑1 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAAccg                                                                                                                                         <  2:658260/150‑1 (MQ=255)             gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGCtc                                                                                                                                   >  2:702004/1‑150 (MQ=255)                     cattcccAGCCGCAGCCGTGTGTCAGCGGCTCCCGGTTTTCTTTC‑CCCCCACCACCCGCGCTTTTACCCACCCCCTTGTGAAAAAATCCCTTCGCGGCGGCTGCCTGCCGGTTTTTTTCCCGCCG‑CAACAAAACCGCCGTtctctc                                                                                                                               <  2:523853/141‑1 (MQ=255)                       aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCagtagt                                                                                                                        >  1:32211/1‑151 (MQ=255)                         tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCCCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                       >  1:236270/1‑150 (MQ=255)                          ccgcccGCGGACGTTTGTCAGCGGCT‑CCGGTATTTATTTCCCCCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCGGCCGGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                       <  2:753068/145‑1 (MQ=255)                              ccGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                 >  2:199734/1‑151 (MQ=255)                                  agccttgtgTCAGCGGCTCCCGTGATTCATTC‑CCGCCAACACCCGCGAATTTATCCACCGCCATGTGAAAAAATGCCTTCGCGGCGGCTGTCTGCCAGTTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                               <  1:485997/144‑1 (MQ=21)                                    aCCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                 >  2:478346/1‑145 (MQ=255)                                      cTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                                 >  2:101517/1‑143 (MQ=255)                                       tgtgTCGGCGGCTCCCGGGATTCATTC‑CCGCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCTTGCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                               <  1:968006/144‑1 (MQ=255)                                         tgtCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGgaa                                                                                                        >  1:73466/1‑149 (MQ=255)                                                     ccGTGTTTCTTCC‑CCCCCAACACCCCCCCTTTTTCCCAACGCCATGTGAAAAAATGCCTCCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGcc                                                                                            <  2:375998/149‑1 (MQ=255)                                                     ccGTGATTCATCC‑CCCCAAACACCCGCGCATTAACCCACCGCCTTGTGCAAAAATGTCTGCGCGCCGGCTGTCTGCCAGAT‑TTTTTCCGGCGAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAg                                                                                              <  2:368900/147‑1 (MQ=255)                                                      cGTTATTCATTC‑CCCCAAACACCCGCGCATTTACCCACCCCCTTGTGAAAAAATGCCTTCGCGGCGGCTGTCGCCCACCTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGt                                                                                         <  1:487381/151‑1 (MQ=255)                                                       gTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGGGaaaaaaaatttaaaccg                                                                                          >  2:270330/1‑135 (MQ=25)                                                            tCATTC‑CCGCAAACACCCGCGATTTTACCCACCCCCATGTGAAAAAATGCTTTCGGGGGGGTTGTCTGCCAGTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAt                                                                                      <  2:639409/148‑1 (MQ=255)                                                                   ccccaaacaccCGCGCTTTTACCCACCCCCATGTAAAAAAATGCCTTCGCGGCGGCTGTCTCCCAGTTTTTTTCCCCCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                                 <  2:62403/142‑1 (MQ=255)                                                                   ccGCCAACACCCGCGCTTTTACCCAACGCCATGTGAAAAAATGCCTTCGCGGCGGCTTTCTGCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTtgtgt                                                                               <  1:46145/149‑1 (MQ=255)                                                                      ccAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAAAAAAAACTTTAAAACCGCCCTGTTTTGTggga                                                                           >  1:457753/1‑148 (MQ=25)                                                                             ccgctcttttccccACCGCCATGTAAAAAAATGCCTCCGCGGGGGCTGTCTCCCATTTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                    <  2:824697/138‑1 (MQ=255)                                                                             ccGCGCATTTACCCACCGCCATGTAAAAAAAGCCCTCCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctg                                                                    <  1:664424/150‑1 (MQ=255)                                                                              cgcgCTTTTACCCAACGCCATGTCAAAAATTGCCTCCGCGGCGGCTGTCTCCCAGCTTTTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                                  <  1:193652/151‑1 (MQ=255)                                                                                 gcttttACCCACCCCCTTGTCAAAAAATCCCTCCGCGGCGGCTGTCTGCCACTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                                <  2:882696/147‑1 (MQ=255)                                                                                   aTTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAAACCGCCATGTTGTGTggggaaagc                                                                      >  1:822451/1‑135 (MQ=37)                                                                                        tCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAAATTTAAAACCCGCCTGTTTTGTGGGGATCACTGCTgggtagaa                                                          >  2:573775/1‑143 (MQ=25)                                                                                              gCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGAAAAAAATTTAAACCCCCCCTGTTTTGTGGGGAACTCTGCTGGGAaaaa                                                          >  1:919281/1‑143 (MQ=25)                                                                                                       aaaaaTGCCTTCGCGGCGGCTTTCTCCCAGTTATTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                                          <  1:908970/150‑1 (MQ=255)                                                                                                       aaaaaGCCCTCCGCGGCGGCTGTCGCCCAGCTTTTTTCCCGCCG‑AAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAg                                            <  2:677178/148‑1 (MQ=255)                                                                                                        aaaagcctcccggggcggtTTTCTGCGACTTTTTTTTCCGCCC‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcg                                        <  2:963846/138‑1 (MQ=255)                                                                                                                 tCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAAAAAATTTTAACCCCCCACGTTGTGTGGGGATCGCCGCTGGGGAAAAAGTGGGAAGGGGAgagggggg                                     >  1:616634/1‑138 (MQ=255)                                                                                                                   ggggcggcTGTCTGCCAGTTTTTTTCCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                 <  1:421538/145‑1 (MQ=255)                                                                                                                        ggcTGTCTGCCTGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGAGGAAAAACTTTAAACCCCCCCCGTTGTGTGGGGATCGCTGCTGGGGAAAAAATGGGAAGGGGAGAgcggcgggacaactcc                           >  2:526941/1‑138 (MQ=255)                                                                                                                        ggcTGTCTCCCAGTTATTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                         <  2:655828/150‑1 (MQ=255)                                                                                                                                 ccAGCTATTTTCCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                       <  2:481233/143‑1 (MQ=255)                                                                                                                                       aTTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCCAGGGAAAAAAATTTTAAACCCCCCTGTTGTGTGGGAAACGCTGCTTGGGAAAATATGGAAAAGGGAGGGGGGGGGGACCGCCCCCGAACCgcgcctattt           >  2:194307/1‑143 (MQ=255)                                                                                                                                         tttcCCGCCG‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt        <  2:591066/150‑1 (MQ=255)                                                                                                                                         tttcCCGCCG‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGt        <  1:309916/150‑1 (MQ=255)                                                                                                                                           tcccgccg‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc      <  1:478400/148‑1 (MQ=255)                                                                                                                                            tCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTTAAACCCCCCTGTTGTGTGGGGATCGCTGCTTGGGAAAAAGTGGGAAGGGGAGGGGGGGGGAACAGCCCCACAACACCGCCAAtt            >  1:25608/1‑143 (MQ=255)                                                                                                                                             ccgccg‑CAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGc    <  1:926353/150‑1 (MQ=255)                                                                                                                                             ccgccg‑AAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc      <  2:670143/148‑1 (MQ=255)                                                                                                                                              ccccg‑cAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt  <  1:124621/149‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                               GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCT  >  NC_000913/357742‑358032

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑