Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	67.6%	6.0 / 35.2	37	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (9/3);  new base A (0/25);  total (9/28)
Fisher's exact test for biased strand distribution p-value = 1.77e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.01e-04

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357742‑358028                                                                                                                                                      |                                                                                                                                              gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaaca                                                                                                                                              <  1:70383/150‑1 (MQ=255)  aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACaaa                                                                                                                                            <  1:824448/151‑1 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgc                                                                                                                                      >  2:328539/1‑151 (MQ=255)              cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTtctc                                                                                                                               >  1:376642/1‑151 (MQ=255)               aTCAGGCAATCCCACCCGCAGCCCTGTGTCAGCGGCTACCGTGATTCATTCCCGCAAACACCCGCGCATTTACCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑ccgccg                                                                                                                                    <  2:250807/145‑1 (MQ=18)                  aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTcc                                                                                                                            >  1:147777/1‑150 (MQ=255)                      aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCagt                                                                                                                         >  1:612930/1‑149 (MQ=255)                              ccGAAGACTTGTGTCGGCGGCTCCCGGATTTCTTTCCCCCCAACACCCGCGCATTTATCAAACGCCTTGTGAAAAATTG‑CCTTCGGGGGGGCTGTCTGCCGGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                                 <  1:323213/149‑1 (MQ=255)                                  aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCggggga                                                                                                             >  1:232576/1‑147 (MQ=255)                                       tgtgTCGGCGGCTCCCGTGATTATTTCCCGCAAACACCCGCGTTTTTACCCACCCCCATGTGAAAAAATC‑CCTTCGGGGGGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAga‑ga                                                                                                       <  1:477690/149‑1 (MQ=255)                                                   tACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                               >  2:878137/1‑130 (MQ=255)                                                           ttCTTTCCCCCCACCACCCGCGCTTTTACCCACCGCCATTGGAAAAAATC‑CCTTCGGGGCGGCTTTCCGCCAGTTTTTTTCCCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAt                                                                                   <  2:382259/149‑1 (MQ=255)                                                            ccagtcccGCAAACACCCGCGCTTTTAACCAACACATTGTAAAAATAGC‑CGTTCGTGG‑GGCTTTCCCCCGGTTTGTTTTCCCTCACAAAAAAATCCGCCGTTCTCTCCAGTAGTGTCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgt                                                                                 <  2:292648/144‑1 (MQ=255)                                                               tcccccccAACACCCGCGCTTTTACCAACCCCCTTGTGAAAAAAGC‑CCTCCGGGGGGGCTGTCGCCCAGTTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCAtgtt                                                                                <  2:17681/142‑1 (MQ=255)                                                                            ccccccttttACCCACCCCCATGTAAAAAAATC‑CTCCCGCGGCGGCTTCCTGCCAGTTTTTTTCCCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                                <  2:202627/144‑1 (MQ=255)                                                                             cgcgattttACCCACCGCAATGTAAAAAATTG‑CCTCCGGGGGGCCGGTCTGCCAGTTTTTTTCCCGCCACAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                               <  2:859327/145‑1 (MQ=255)                                                                                gtttttACCCAACGCCTTGTGCAAAATTG‑CCTTGGCGGCGGCTGTCTGCCGGTTATTTTCCCGCCCCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTgg                                                             <  1:799237/147‑1 (MQ=255)                                                                                  aTTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGA‑GAAAAAACTTTAAAACCCCCATGTTTTGTGGGAATTgc                                                                   >  1:346209/1‑142 (MQ=37)                                                                                   tttACCCACCCCCTTGTGAAAAAATC‑CCTCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                                          <  1:228028/150‑1 (MQ=255)                                                                                        ccaccccaggttgaaaaaaGC‑CCCTCGGGGCGGCTGTCGGCCAGTTTTTTCCCCCCCAAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAtg                                                    <  2:308268/136‑1 (MQ=255)                                                                                        ccACCGCCATGGAAAAAATTC‑CCTCCGCGGCGGTTTTCAGCCTTTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAt                                                     <  2:396193/149‑1 (MQ=255)                                                                                          accGCCATGTGAAAAAATG‑CCTCCGGGGGGCCTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAtgtg                                                  <  1:737834/148‑1 (MQ=255)                                                                                          accGCCATGTGAAAAAAGC‑CCTTCGGGGCGGTTTTCTCCCATTTTTTTTCCCCCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTgg                                                 <  1:959986/149‑1 (MQ=255)                                                                                          accGCCATGTAAAAAAATG‑CCTCCGGGGCGGCTGTCTGCCATTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTgg                                                 <  1:337629/149‑1 (MQ=255)                                                                                           aaccccatttaaaaaaTGCCCTGCGGGGGGGTTTTCGGCCAGTTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AAtgtg                                                  <  2:921701/139‑1 (MQ=255)                                                                                             cccttgtgAAAAATTG‑CCTTCGGGGCGGCTTTCTGCCAGCTATTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGaa                                               <  1:495312/146‑1 (MQ=255)                                                                                              ccATGTGCAAAAATG‑CCTTCGGGGGGGCTTTCGGCCAGCTATTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGaaa                                              <  1:243422/150‑1 (MQ=255)                                                                                                      aaaaaTG‑CCTTCGCGGCGGCTGTCTGCCAGTTTTTTTCCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTg                                      <  1:28125/150‑1 (MQ=255)                                                                                                      aaaaaTG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAATTTTAAACCC‑TCCCGTTTTTTGGGAAAAGCTGCTGGGGACAAAATTGGAAAGGGagggg                                      >  2:949599/1‑147 (MQ=255)                                                                                                      aaaaaTG‑CCTGCGGGGCGGTTGTCTCCCAGTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTAGAAAGGGAAGTgc                                     <  2:832318/151‑1 (MQ=255)                                                                                                                  cgcgGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAACCTTTAAGCCC‑TCCTGTTGTGTTGGGATCGCTTCTGGTGAC‑AACATGGGAAGGGGAGGggggcggggt                             >  1:447839/1‑144 (MQ=255)                                                                                                                   gcggcgGCTGTCTGCCAGCTTTTTTCCCGCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATc                             <  1:471768/147‑1 (MQ=255)                                                                                                                     gggggcTGTCACCCGGTTTTTTTCCCCCCGCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCa                            <  1:810345/143‑1 (MQ=255)                                                                                                                     ggcgggTTTCTGCCATTTTTTTTCCCGCCAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCa                            <  2:1250/146‑1 (MQ=255)                                                                                                                     ggcggcTGTCGGCCGTTTTTTTTCCCGCCGAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTATGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCt                         <  1:973028/149‑1 (MQ=255)                                                                                                                        gggtttcctccAGCTATTTGCCCGCCGCAAAAAAT‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTgcggc                                  <  1:70372/128‑1 (MQ=255)                                                                                                                                           tcccgccgCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  1:252058/148‑1 (MQ=255)                                                                                                                                             ccgccaCAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTc  <  2:415505/148‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                              GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATG‑CCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGA‑GAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAC‑AATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAGTTC  >  NC_000913/357742‑358028

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑