Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	43.1%	61.2 / 25.4	51	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (18/11);  new base T (0/22);  total (18/33)
Fisher's exact test for biased strand distribution p-value = 2.35e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357728‑358015                                                                                                                                                          |                                                                                                                                                gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTAttt                                                                                                                                              >  1:1259112/1‑151 (MQ=255)  aaCTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTAtttt                                                                                                                                             <  2:307671/151‑1 (MQ=255)      cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccg                                                                                                                                        <  2:932311/151‑1 (MQ=255)       gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccgc                                                                                                                                       <  1:1062436/151‑1 (MQ=255)       gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccgc                                                                                                                                       >  2:277874/1‑151 (MQ=255)        tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccgcc                                                                                                                                      >  2:57539/1‑151 (MQ=255)        tAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccgcc                                                                                                                                      >  1:518240/1‑151 (MQ=255)         aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑ccgcc                                                                                                                                      <  1:695897/150‑1 (MQ=255)                aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGcaacaa                                                                                                                               <  2:1144613/150‑1 (MQ=255)                aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                              <  1:646499/151‑1 (MQ=255)                aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                              <  2:1054938/151‑1 (MQ=255)                 tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACaaa                                                                                                                              >  2:192340/1‑150 (MQ=255)                     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgc                                                                                                                         >  1:1171240/1‑151 (MQ=255)                     cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccg                                                                                                                          <  2:1078427/150‑1 (MQ=255)                        aGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGt                                                                                                                      >  1:1037005/1‑151 (MQ=255)                         gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAAccgccg                                                                                                                       <  1:768133/149‑1 (MQ=255)                               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                               >  2:408317/1‑151 (MQ=255)                                 ggCATTTCCGGCCCCAGCCCTTTGTCGGCGGCTCCCGTTTTTCTTTC‑CCCCA‑AACACCCGCGCTTTTATCCAC‑CCCCA‑TGTCCAAAAATCCCTTC‑GGGGCGGCTG‑TCTCCCAGCTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCag                                                                                                             <  1:1198153/151‑1 (MQ=255)                                   cattcccAGCCGCAGCGTTGTGTCAGCGGCTACCGTGTTTCTTCC‑CCGCC‑AACAACCGCGCATTTATCCAC‑CGCCA‑TGTGCAAAAATGCCGTC‑GGGGCGGCTG‑TCTGCCATTTTTTTTT‑CCCCCGCAACAAAACCGCCGTtctctc                                                                                                                <  2:1276174/141‑1 (MQ=255)                                     aTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCGG‑TCTGCCAGCTATTTTT‑CCACCGCAACAAAACCGCCGTTCTCTCCagta                                                                                                           >  2:77627/1‑149 (MQ=255)                                        ccccccGCAGCCTTGTGTCAGCGGCTCCCGTTTTTCATTC‑CCCCC‑ACCACCCCCCCTTTTCCCCAC‑CCCCA‑TGTAAAAAAATCCCTCC‑GCGGCGGCTG‑CCTGCAAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCagta                                                                                                           <  2:31752/142‑1 (MQ=255)                                          aGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                    >  1:768704/1‑151 (MQ=255)                                            ccGAAGCCCTGTGACAGCGGCT‑CCGGTATTTATTTCCCCCC‑AACACCCGCCCTTTTACCCAC‑CCCCT‑TGTGAAAAAATGCTTTC‑GGGGGGGCTG‑TCTGCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                    <  1:52819/149‑1 (MQ=255)                                               ctgccttgtgTCGGCGGCTTCGGTGATTCATTT‑CCGCC‑AACACCCGCTCTTTTAACCAC‑CGCTA‑TTTAAAAAACTGCCTCG‑GCGGCGCCTC‑TCTGCGATCTATTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                <  1:311717/144‑1 (MQ=255)                                                   cttgtgCCAGCGGCCCCCCTGATTCTTTC‑CCCCC‑AACACCCGCGCATTTACCCAC‑CGCCA‑TGTGAAAAAATG‑CTTC‑GGGGGGGCTGTTCGGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCaa                                                                                               <  2:1081003/145‑1 (MQ=255)                                                   ccTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                   >  1:991877/1‑143 (MQ=255)                                                      gtgtCGGCGCCTCCCGTGATTCTTTC‑CCCCA‑AACACCCGCGTTTTTACCCAC‑CCCCT‑TGTAAAAAAAGCCCTCC‑GCGGGGGCTG‑TCGGCCAGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                          <  2:113503/148‑1 (MQ=255)                                                      gtgtCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggacgtaga                                                                                          >  2:327771/1‑141 (MQ=255)                                                        gccAGCGGTTCCCGTGATTCTTTC‑CCCCC‑AAAACCCGCCCTTTTACCCAC‑CCCCT‑TGTGAAAAAAGGCTTCC‑GGGGGGGCTT‑TCTGCCAGTTTTTTTC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAgag‑a                                                                                          <  1:1242738/144‑1 (MQ=255)                                                               ggctcccgtttttaTTT‑CCCCCAAACACCCGCGAATTT‑TCCAACCGCCA‑GGTAAAAAAATCCTTCC‑GGGGCGCTTG‑TCTCCCATTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAagag                                                                                            <  1:377618/126‑1 (MQ=255)                                                                ctcccgtttttCTTTC‑CCCCC‑ACCACCCGCCCTTTTACCCAC‑CCCCT‑TTTCAAAAAATCCTTCC‑GCGGCGGCTT‑TCTCCAAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGcggg                                                                                 <  1:408735/138‑4 (MQ=255)                                                                cTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑aaaaaaa                                                                                    >  1:300445/1‑140 (MQ=255)                                                                 tACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGTGGAaggaaaaaaacattta                                                                                >  1:632960/1‑134 (MQ=25)                                                                   ccttatttCATTC‑CCGCC‑ACCACCCGCGTTTTTATCCAC‑CCCAA‑TGTGAAAAAAGGCCTGC‑GGGGCGGCTT‑TCGGCCAGCTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGccc                                                                           <  1:1034467/144‑1 (MQ=255)                                                                      tttttCTTTC‑CCCCC‑ACCACCCGCTCTTTTACCAAA‑CCCTT‑TGTAAAAAAATGCCTCC‑GCGGGGGTTG‑TCT‑CCAGGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTc                                                                        <  2:803179/147‑1 (MQ=255)                                                                      tGATTCTTTC‑CCCCA‑AACACCCCCGATTTTACCCAC‑CGCAT‑TGT‑CAAAAATTCCCTCGGCGGGGGCTG‑TCGGCAAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGt                                                                         <  2:1226909/149‑1 (MQ=255)                                                                                  ccccaaacaccCGCGCTTTTACCCAC‑CCCCT‑TGTAAAAAAATGCCTTC‑GCGGCGGTTG‑TCTGCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTtgtgtg                                                              <  1:102361/145‑1 (MQ=255)                                                                                      caaacaccccctaTTTAACCAACCGCCA‑TTTAAAAAATTCCCTCC‑GGGGCGGCTT‑TCTGCCAGTTTTTTTC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                          <  1:562494/139‑1 (MQ=255)                                                                                       accacccGCGCTTTTA‑CCAA‑CCCCATTGTAAAAAAAT‑CCTTCGGGGGCGGTTG‑TCTGCCGGTTTTTTTC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCaa                                                          <  2:1279175/144‑1 (MQ=255)                                                                                              gcgcATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAG‑AAAAAACATTAAAACCCTCCAGTTGTggggggaaag                                                       >  1:133189/1‑139 (MQ=25)                                                                                               cccttttACCCAC‑CCCCA‑TGGAAAAAAATCCTTCC‑GGGGCGGCTG‑TCTCCCAGTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                <  1:992909/147‑1 (MQ=255)                                                                                                         cccaccgcctttagaaaaaaTCCCTTC‑GCGGCGGCTG‑TCCGCCACTTTTTTTC‑CCGCCGCAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAAt                                        <  1:1711/135‑1 (MQ=255)                                                                                                                        aaaaaTGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAG‑AAAAAACTTTTAACCCCTCACGTTTTGTTGGTCTCGCTCCTCGTGAACAA‑GTGGGAAGGGGAgag                         >  2:167779/1‑148 (MQ=255)                                                                                                                         aaaaTGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCGCGAGAAAAAAATTTTAAACCCCCCA‑GTTGTGTGGGGAACGCCGCTGGG‑GAAAAAGTGGGAAGGGGAgaggg                       >  1:240995/1‑147 (MQ=255)                                                                                                                          aaaTGCCTCG‑GGGGGGGTTT‑TCGGCCAGTTTTTTTC‑CCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTgcgg                      <  1:745586/151‑1 (MQ=255)                                                                                                                                     gggggggcTG‑TCGGCCGTTTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCa               <  2:1186843/143‑1 (MQ=255)                                                                                                                                     ggggcggcTG‑TCTGCCGTCTTTTTTC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAg              <  2:376923/147‑1 (MQ=255)                                                                                                                                       ggcggcTT‑TCTGCCACTTTTTTTC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATc                <  1:1227983/145‑1 (MQ=255)                                                                                                                                          ggcTG‑TCGCCCAGTTATTTTC‑CCGCCGAAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg        <  1:364959/150‑1 (MQ=255)                                                                                                                                             tG‑TCTGCCATTTTTTTTC‑CCGCCCCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa       <  2:509482/148‑1 (MQ=255)                                                                                                                                                 cTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAG‑AAAAAACTTTTAACCCCGCCTGTTGTGTGGGAAACGCCGCTGGG‑AAAAAAGTGGGAAGGGGAGGGGGGGGGATCAACTCCCCAAcccc  >  1:812105/1‑148 (MQ=255)                                                                                                                                                          |                                                                                                                                                GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTT‑CCGCC‑AACAACCGCGCATTTATCCAA‑CGCCA‑TGTGCAAAAATGCCTTC‑GCGGCGGCTG‑TCTGCCAGCTATTTTT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAG‑AAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGT‑AACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357728‑358015

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: ‑