Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,875	0	A	T	38.1%	54.3 / 14.0	43	N272K (AAT→AAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base A (13/13);  new base T (1/15);  total (15/28)
Fisher's exact test for biased strand distribution p-value = 5.82e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  NC_000913/357728‑358015                                                                                                                                                     |                                                                                                                                                gAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                                <  1:73160/149‑1 (MQ=255)  aaCTCGTCTGCCTCTTATGCGTGGCGCACCAGGCTCTTCCCACCGCCCCCCCGTGTCACCCGCCCCCTTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTAt                                                                                                                                                <  1:27723/148‑1 (MQ=9)   ccgcgtcgcccTGATAAGCGTAGCGCATCATGCACTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTAttttt                                                                                                                                            <  1:527467/142‑1 (MQ=14)    cTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTc                                                                                                                                           >  1:888651/1‑151 (MQ=255)      cGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTccg                                                                                                                                         <  2:149086/151‑1 (MQ=255)       gTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTccgc                                                                                                                                        >  2:806756/1‑151 (MQ=255)         aGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTccgcc                                                                                                                                       <  2:1038837/150‑1 (MQ=255)           gCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCcgccg‑c                                                                                                                                    >  1:662642/1‑150 (MQ=255)               gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑caacaa                                                                                                                               <  1:766404/151‑1 (MQ=255)                aTAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTCTCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑caaca                                                                                                                                <  1:899015/149‑1 (MQ=255)                  aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaaa                                                                                                                             <  2:661385/150‑1 (MQ=255)                  aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaaa                                                                                                                             >  1:746245/1‑150 (MQ=255)                         gcgcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGtt                                                                                                                    >  2:4199/1‑151 (MQ=255)                           gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTtct                                                                                                                  >  2:1030859/1‑151 (MQ=255)                                 ggCAATTCCAGCCGCTGATCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTCTCCAACGCCATGTGCAAAAATGCC‑TTCGCAGCGGCTGTCTGCCAGCTGTTTTTTCGGCC‑CAACACAA‑cgtgcactccttcc                                                                                                              >  1:104421/1‑136 (MQ=11)                                      tcccAGCCCAAGCCCGGTGTCAGCGCCTCCCGTGTTTCATTCCCCCCACCACCCGCCCATTTACCCAACGCCATGTGAAAAAAGGCC‑TTCGCGGCGGCTGTCTGCCATTTATTTTCCCCCCG‑AAAAAAAA‑CCGCCGTTCTCTCCagtagt                                                                                                        <  2:889085/148‑1 (MQ=255)                                           gCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑ggg                                                                                                 >  2:262727/1‑151 (MQ=255)                                               ccgACCAGTGTCAGCGGCTACCGGGATTCATTTCCGCCAAAAAACGCGCATTTATCCAACGCCATGTGCAAAAACGCC‑TTCGCGTCGGATTTCTCCTAGCTTTTCTTCCGCCC‑CAACCAAA‑CCCCCGTTCTCTCCAGTAGTTGC‑g                                                                                                   >  1:752381/3‑145 (MQ=255)                                                agcttgtggccAGGGGCTGCCGTGATTCTTCCCCGCAACCACCCGCGCTTTCACCCACCGCGTGGTGAAAAATGGCC‑TCGGGGGGGGCTGTGTGCCGGTTTTTTTCCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑gggg                                                                                                <  1:505485/137‑1 (MQ=255)                                                  aCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑ggggg                                                                                               >  2:611231/1‑145 (MQ=255)                                                   ccTGTGTCAGCGGCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCATTTACCCACCGCCTTGTGAAAAAATGCT‑TTCGCGGGGGCTGTCGGCCAGTTTTTTTCCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAagag                                                                                          <  2:758206/150‑1 (MQ=255)                                                               gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGaaaaaacatt                                                                                >  2:1088995/1‑141 (MQ=255)                                                                  aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGAGGAGgaaaaacagttaaacc                                                                          >  1:89250/1‑138 (MQ=25)                                                                   ccGTGTTTCATTCCCGCCAACACCCGCGCTTTTACCCAACGCCATGGGAAAAAATGCC‑TCCGCGGCGGCTGTCTGCCAGCTATTTTCCCGCCG‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCttt                                                                                <  1:218585/144‑1 (MQ=255)                                                                         ttattccccGCCACCACCCGCGTATTTCCCCAACGCCTTGTGAAAAAAGGCG‑TCCGGGGGGGCTGTGT‑CCCGTTTTTTTTCCCCCGAAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGc                                                                                   <  1:867816/128‑1 (MQ=255)                                                                         ttCATTCCCCCCAACACCCGCGCATTTACCCACCCCCATGTGAAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGTTATTTTCCCGCCG‑CAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCa                                                                      <  2:164891/148‑1 (MQ=255)                                                                                     aacaccCGCGCTTTTACCCACCCCCATGGGAAAAATTGCT‑TCCGCGGCGGCTGTCTCCCAGTTTTTTTCCCGCCG‑CAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                       <  2:480989/151‑1 (MQ=255)                                                                                        acccccgcATTTACCCACCGCAATTGGAAAAACTCCC‑TTCGCGCCGGTTGTCTGCCACCTTTTTCCCCCCCG‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATc                                                       <  2:689820/143‑1 (MQ=255)                                                                                          ccGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAGAGAAA‑AACATTAAAACCCTCATTTTTTGTgg                                                            >  2:159949/1‑141 (MQ=25)                                                                                          ccGCCCATTTATCCACCGCCATGTGAAAAAATCCC‑TTCGGGGCGGCTGTCTGCCAGTTTTTTTCCCGCCG‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgc                                                  <  2:304672/151‑1 (MQ=255)                                                                                                      cccacccacgtggaaaaaaGGCCGTTGGCGGCGCTTGTCTGCCATGTTTTTTCCCGCCG‑‑AACAAAATCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgctgct                                                 <  1:4198/127‑1 (MQ=255)                                                                                                          ccccATGTAAAAAAATGCC‑TGCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCG‑CAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                   <  2:597492/148‑1 (MQ=255)                                                                                                             cATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGAAAAAAATTTTAAACCGCCCCGTTTTGTGGGGATCGCTGCTGGGTACAATGTggg                                   >  2:752614/1‑146 (MQ=25)                                                                                                               tgtgAAAAAATGCT‑TTCGCGGCGGTTTTCTGCCAGTTTTTTTCCCGCCG‑CAACAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAggg                              <  2:666204/150‑1 (MQ=255)                                                                                                               tgtgAAAAAATGCC‑TTCGCGGGGGCTTTCTCCCAGTTTTTTTCCCGCCG‑CAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAgg                               <  2:104464/149‑1 (MQ=255)                                                                                                                   aaaaaaTGCC‑TCCGGGGCGGCTGTCTGCCAGTTTTTTTCCCCCCG‑CAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTg                         <  2:894436/150‑1 (MQ=255)                                                                                                                    aaaaaTGCC‑TGCGCGGCGCGTGTCTCCAAGTTTTTTTCCCCCCA‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGt                          <  1:13699/149‑1 (MQ=255)                                                                                                                     aaaaccgcctcgggggcgtcTGTCGCCCAGTTTTTTTCCCCCCG‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                        <  1:473860/137‑1 (MQ=255)                                                                                                                           gctgtcggggggcatGTCGGCCACTTTTTTTCCCGCCC‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                      <  2:517944/133‑1 (MQ=255)                                                                                                                           cc‑TGCGGGGCGGCTTTCTGCCATTTTTTTTCCCCCCG‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGa                   <  2:534251/149‑1 (MQ=255)                                                                                                                                      ggttgtcggcggtttATTTTCCCGCCG‑AAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGc             <  1:816153/131‑1 (MQ=255)                                                                                                                                         tGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGGGAAAAAACATTTAACCCCCCCTGTTTTGTGGGGATCGCTGCTGGGTAAAAAGTGGGAAGGGGAGGGGGGGGGAACAGCCCCaca       >  2:154091/1‑146 (MQ=255)                                                                                                                                               caagttATTTTCCCGCCG‑AAACAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcgc  <  1:966194/142‑1 (MQ=255)                                                                                                                                                     |                                                                                                                                                GAACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGC  >  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 < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑