Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	39.3%	39.3 / 11.7	28	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (12/5);  new base T (0/11);  total (12/16)
Fisher's exact test for biased strand distribution p-value = 2.53e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCG  >  NC_000913/357733‑358016                                                                                                                                                  |                                                                                                                                                cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑cc                                                                                                                                        <  1:921167/150‑1 (MQ=255)    aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑ccgccg                                                                                                                                    >  1:1069625/1‑151 (MQ=255)    aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑ccgccg                                                                                                                                    <  1:762876/151‑1 (MQ=255)        cTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGcaac                                                                                                                                >  2:668456/1‑151 (MQ=255)            tAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACaaa                                                                                                                             >  2:853039/1‑150 (MQ=255)              aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAAcc                                                                                                                          <  2:537834/151‑1 (MQ=255)              aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAAcc                                                                                                                          >  2:1024913/1‑151 (MQ=255)               gCGTACCGCATCAGGCAATTCCAGCCTCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACaaaa                                                                                                                            <  2:1092529/148‑1 (MQ=255)                           aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                              >  1:585077/1‑150 (MQ=255)                             gCAATTCCAGCTGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAACTGCC‑TTCGCGGCGGCTGTCTGCC‑AGCCATTT‑TT‑CTGCCGCAACAAAACCGCCGTTCTCTCCagt                                                                                                           >  1:876230/1‑151 (MQ=255)                                  tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                      >  2:1179281/1‑151 (MQ=255)                                   cccgCCGCAGTCTTGTGTCGGCGGCTCGGGTTATTCATCCCCCCCAACACCCGCGCTTTTA‑CCAACCCCAGGGTGAAAAAAGGCC‑TCCGGGGCGG‑TTTCCGCCAAGTTTTTT‑TC‑CCCCCGAAAAAAAACCGCCGTTCTCTCCagtagt                                                                                                        <  1:679997/145‑1 (MQ=255)                                           aGACCTGTGTCAGCGGTTCCTGTGTTTCTTTCCCGCAAACACCCGCCTTTTTACCCACCGCCA‑TGTAAAAAAATCCC‑TTGGGGGCGCCTGCCGCCA‑ATCTTTTT‑TC‑CCGCCGCAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                               <  2:763734/149‑1 (MQ=255)                                             ccgtggcgcAGGGGCCACCGTGATTATTTTCCGCCAACACCCCGGCTTTTGTCCACCGCAT‑TGTAAAAAATGGCC‑TTGCCGGCGGTTGTCCCCC‑CGCTTTTT‑TT‑CCCCCCCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAag                                                                                             <  2:107100/141‑1 (MQ=255)                                                      aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAGAtt                                                                                  >  2:1136581/1‑151 (MQ=255)                                                      aGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAGAGaaaaa                                                                                      >  2:216937/1‑145 (MQ=255)                                                        cGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAgggagaaaaaatt                                                                                 >  1:1161639/1‑141 (MQ=255)                                                              cggggATTCTTTCCCCCCAACACCCACGCATTTCCCCACCCCAA‑TGTGCAAAAAGGCC‑TGCGCGCCGGCTGTC‑GCC‑CGCTTTTT‑TTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATa                                                                                      <  2:381252/135‑1 (MQ=255)                                                                                     ccccctttttACCCACCGCTG‑TGTAAAAAAATCCC‑TGCGCGCCGTTTGTCCCCC‑AGTTTTTT‑TC‑CCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                     <  1:339831/142‑1 (MQ=255)                                                                                      cgcgCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGAAAAGAAAAAAATTTAAAACCCCCCTGTTTTGTgggga                                                          >  2:941478/1‑140 (MQ=25)                                                                                       gcgtttttgcccgaCGCGA‑TGTACAAAAGTCCC‑TTCGCGGCGTGT‑TCCGCC‑TGTTTTTTGTT‑CCGCCGCAAGAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                  <  2:877399/137‑1 (MQ=255)                                                                                             tcaTCCAACCCCC‑AGTTCAAAAAGGCC‑TTCCGGGCCGGTGTCGGCCGATTTTTTT‑TC‑CCGCCAAAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTaa                                             <  1:228937/148‑1 (MQ=255)                                                                                                tCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGGAAAAAATTTTAACCCCTCATGTTTTGTGGGGATAGCTGCTTGGAACaa                                          >  2:31213/1‑149 (MQ=25)                                                                                                              aaaaaaaTCCC‑TCCGGGGGGTCTGTCGCCG‑AGTTTTTT‑TC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                           <  1:315467/149‑1 (MQ=255)                                                                                                                aaaaaTTCCTTTCGCGGGGGCTTTCTCCC‑AGTTATTT‑TC‑CCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                          <  2:824031/151‑1 (MQ=255)                                                                                                                                gcggcTTTCTGCC‑AGTTTTTT‑TC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                 <  2:443043/144‑1 (MQ=255)                                                                                                                                       tCTGCC‑AGTTTTTT‑TC‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAcc     <  2:390013/149‑1 (MQ=255)                                                                                                                                           cc‑AGTTTTTT‑TC‑CCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgcg  <  2:475830/148‑1 (MQ=255)                                                                                                                                                  |                                                                                                                                                CGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCA‑TGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCC‑AGCTATTT‑TT‑CCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCG  >  NC_000913/357733‑358016

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑