Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	53.1%	24.1 / 75.7	49	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (15/8);  new base A (0/26);  total (15/34)
Fisher's exact test for biased strand distribution p-value = 3.11e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.25e-06

TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357744‑358034                                                                                                                                                        |                                                                                                                                                    tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACaaa                                                                                                                                                  >  1:1145391/1‑150 (MQ=255)  aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAAc                                                                                                                                                <  2:898811/151‑1 (MQ=255)  aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAAc                                                                                                                                                >  1:747380/1‑151 (MQ=255)       ttgcccATCACGCAACTCCAGCCGCAGACCTGTGTCAGCGGCTCCCGTGATTCATTCCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAAcc                                                                                                                                               <  2:262774/142‑1 (MQ=18)           gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTtct                                                                                                                                       >  4:432392/1‑151 (MQ=255)               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTcc                                                                                                                                   >  3:335910/1‑151 (MQ=255)               cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTcc                                                                                                                                   >  2:362887/1‑151 (MQ=255)                    atttCCAGCCGAAGCCTTGTGTCAGCGGCTCCCGTGATTCTTTCCCCCAAACAC‑CCGCGTTTTTATCCAACCCCTTGTGAAAAAATCCCT‑CGGCGG‑CGGCTGTCTGCCACTTTTTTTC‑CCGCCCA‑AAAAAAACCGCCGTTCTCTCCagtag                                                                                                                              <  1:1091573/149‑1 (MQ=255)                      tcccACCCGCAGCCCTGTGCCAGCGGCTACCGTGATTCATTCCCGCCAACAC‑CCGCGAATTTACCCAACGCCATGTGAAAAAATGCCT‑CCGCGG‑CGGCTGTCTGCCAGTTATTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCagta                                                                                                                               <  4:395173/146‑1 (MQ=18)                       cccACCCGCAGCCCTTTGCAGGGGGCTCCGGTGATTCTTTCCCCCCAACAC‑CCGCGCTTTTCCCCAACCCCTTGTCAAAAAATCCCT‑CCGGGC‑CGGCTGCCTGCCATTTTTTTTC‑CCCCCGA‑AACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                                           <  1:1038691/150‑1 (MQ=255)                            ccGCAGCCTTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCCAACAC‑CCGCGCTTTTACCCACCGCCATGTAAAAAAATGCCT‑CCGGGG‑CGGTTGTCTCCCAGTTTTTTTC‑CCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        <  1:619855/149‑1 (MQ=255)                            ccGCAGCCTTGTGCCGGCGCCTCCCGTATTTCTTTCCCCCCACCAC‑CCCCGCTTTTACCCACCCCCAT‑TAAAAAAAAGCCTGCCGCGG‑CGGTTTCCCGCCAGTTTTTTTC‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       <  2:1271924/150‑1 (MQ=255)                            ccGCAGCCCTGTGTCGGCGGCTCCCGTTTTTC‑TTTCCCCCAAAAACCCGCGCATTTACCCAACGCCTTGTGAAAAAATCCCT‑CCGGGG‑GGGTTGTCTGCCAGTTTTTTTC‑CCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        <  4:203725/149‑1 (MQ=255)                            ccGCAGACCTGTGTCGGCGCCTACCGTTATTCATTCCCCCAAACAC‑CCGCGCTTTTACCCACCCCCATGTCAAAAATTGCTT‑CCGCGG‑CGGCTGTCGGCCGGTTTTTTTC‑CCCCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                        <  1:300429/149‑1 (MQ=255)                             cGCAGCCGTGTGTCGGCGTTTACCGTGTTTCTTTCCCCCCAAAAC‑CCGCGCATTTACCCAACCCAATGTGAAAAAATGCCT‑CCGGGG‑GGGCTGTCTGCCCGTTTTTTTC‑CCCCCAA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                                         <  1:665663/147‑1 (MQ=255)                                    cTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCgggggc                                                                                                                    >  1:874963/1‑143 (MQ=255)                                      gtgtCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑Gaaa                                                                                                            >  1:116974/1‑150 (MQ=255)                                       tgtCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGGGA‑Gaaa                                                                                                            >  1:398091/1‑149 (MQ=255)                                             cGGCTCCCGTGTTTCATTCCCGCCAACAC‑CCGCGCATTTACCCACCCCCATGTGCAAAAATGCTT‑TCGGGG‑CGGCTTTCGCCCAGTTTTTTTC‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCggg                                                                                                                       <  4:303011/133‑1 (MQ=255)                                                     gTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑Gaaaaaaattttaacccc                                                                                              >  1:1234626/1‑135 (MQ=25)                                                       gATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGgaaa‑gaaaaaaattt                                                                                                     >  1:570421/1‑133 (MQ=25)                                                       gATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGA‑Gaaaaaaattttatc                                                                                                 >  4:179866/1‑133 (MQ=25)                                                         ttCTTTCCCCCCAACAC‑CCGCGC‑TTTTCCCCACCCCATGGGGAAAAAAGCCT‑TTGGGGCCGTCTGTCTGCCAGTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGc                                                                                                 <  1:62727/142‑1 (MQ=255)                                                             ttccccccAACAA‑CCGCGCTTTTACCCACCCCCATGTAAAAAAAGCCCT‑CCGGGG‑GGGCTGTCTGCCAGTTATTTTC‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgttg                                                                                      <  1:206885/143‑1 (MQ=255)                                                                ccccaaacaa‑cGGCGCATTTATCCACCGCCATGTGAAAAAATGCCT‑TCGGGG‑CGGCTGTCTGCCATTTTTTTTC‑CCGCCGA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTtgtg                                                                                    <  1:457607/143‑1 (MQ=255)                                                                        cacccGCGTGTTTCTCCAACGCCATCCGCAAAAAGTCCT‑AGGCGG‑CGGCGGTCCGCCGTCTTTTTTT‑CCACCAC‑AAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑g                                                                          <  1:859567/147‑1 (MQ=255)                                                                           ccccctatatccccACCGCTATGTACAAAATTGCTT‑CCGGGG‑CGGCTGTCCGCAGGTTATTTGC‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑g                                                                          <  1:1195709/135‑1 (MQ=255)                                                                                  tttATCAACCGCCATGTAAAAAAATGCCT‑GCGGGG‑CGCCTGTCTGCCAGTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑Gctgct‑g                                                                   <  1:95084/146‑1 (MQ=255)                                                                                        cAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAAAAATTTTTAACCCTCATGTTGTGTGGGGATC‑GGTGCC‑GGGGAAAAtgt                                                         >  4:90960/1‑150 (MQ=25)                                                                                           ccccttgtgAAAAATTCCCT‑CCGCGG‑CGGTGTTCTGCCAGCTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAAtgt                                                         <  2:130410/142‑1 (MQ=255)                                                                                                    aaaaaaTGCCT‑GCGGGG‑CGGCTGTCGCCAATTTATTTTC‑CCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTg                                            <  1:764244/150‑1 (MQ=255)                                                                                                    aaaaaaTCCCT‑CCGCGG‑CGGTTTTCTCCCAGTTTTTTTC‑CCGCCAC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGaa                                               <  2:901297/147‑1 (MQ=255)                                                                                                     aaaaaTCCCT‑CCGCGG‑CGCCTGTCTGCCATTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGt                                             <  2:1043787/149‑1 (MQ=255)                                                                                                                tCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAA‑GGAAAAACTTTTAACCCGTCCTGGTGTGTGGGCATCGGCGGCG‑GTGAAAAAAGTGGAAAgggggggggggg                                        >  2:461636/1‑136 (MQ=255)                                                                                                                tCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAAAAGATTTTAATCCCTCCTGCTGTTTGGGGAAC‑GCTGCTGGGTAAAAACTTGGGAGGGGAAgggggg                                         >  2:465247/1‑139 (MQ=255)                                                                                                                  gcgg‑cgGTTGTCTCCCAGTTTTTTTC‑CCCCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCa                                  <  1:34922/148‑1 (MQ=255)                                                                                                                  gcgg‑cgGCTCTCGCCCAGTTATTTTC‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAg                                 <  2:398024/149‑1 (MQ=255)                                                                                                                    gg‑cggcTGTCTGCCATTTTTTTTC‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGGGGCGAATCAGCTc                              <  1:417086/150‑1 (MQ=255)                                                                                                                     gggggcTTTCTGCC‑GCTTTTTTTCCCGCCCA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                                   <  3:93381/142‑1 (MQ=255)                                                                                                                        ggctgccgcccAGTTTTTTTC‑CCGCCGA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAg                           <  1:476685/141‑1 (MQ=255)                                                                                                                        ggcTTTCTCCCAGTTTTTTTC‑CCGCCGC‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                            <  1:73988/149‑1 (MQ=255)                                                                                                                        gcctgccgcccAGTTTTTTTC‑CCGCCAA‑AAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAAt                                    <  3:66087/132‑1 (MQ=255)                                                                                                                              cggCCAGCTTTTTTC‑CCGCACA‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGaa                         <  2:1056695/144‑1 (MQ=255)                                                                                                                              cgcccgctttttttc‑CCGCCAA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCa                            <  2:708278/133‑1 (MQ=255)                                                                                                                                       tttttt‑CCCCCCCAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCt                  <  2:419285/144‑1 (MQ=255)                                                                                                                                           tt‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGCGGGAGAGGAAAAACTTTTAAGCCC‑TCCCTTTTTTTGGGAATC‑CCCGCT‑GGGGAAAAAATGGGAAGGGAAGAGGGGGGGATCAGCCCCCCAACACCGCCAATTTAGt          >  1:972247/1‑148 (MQ=255)                                                                                                                                              ccgccgA‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCg       <  4:318170/149‑1 (MQ=255)                                                                                                                                               cgccgc‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCt    <  4:9950/151‑1 (MQ=255)                                                                                                                                                 ccgc‑AAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCa  <  4:406930/151‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                    TAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAA‑CCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGG‑CGGCTGTCTGCCAGCTATTTTT‑CCGCCGC‑AACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATC‑GCTGCT‑GGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTCGCCTCA  >  NC_000913/357744‑358034

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: ‑