Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,880	0	T	C	47.5%	40.3 / 10.9	40	K271E (AAA→GAA)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base T (15/6);  new base C (0/19);  total (15/25)
Fisher's exact test for biased strand distribution p-value = 1.45e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357730‑358025                                                                                                                                                        |                                                                                                                                                      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                                                                                                                                        >  1:746245/1‑150 (MQ=255)                aaGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACaaaa                                                                                                                                        <  2:661385/150‑1 (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‑‑AACAAAAT‑CCGCCGTTCTCTCCAGTAGTGGC‑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)                                                                                                                                                    tttttCCGCCC‑CAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg  <  2:898779/150‑1 (MQ=255)                                                                                                                                                    tttttCCCCCC‑CAAAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTc                     <  1:791160/133‑1 (MQ=255)                                                                                                                                                    ttttcCCGCCG‑AAAAAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg    <  2:415270/148‑1 (MQ=255)                                                                                                                                                     ttttCCCCCA‑CAAAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGGAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGa   <  2:874905/149‑1 (MQ=255)                                                                                                                                                      tttCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCAGAGAAAAAAATTTTAAACCGTCCTGTTGTGTGGGGAACCCCGCTGGGGACAAAGTGGGAAGGGGAGGGGGGGGGAACAACTCCAAAAACGCCCCAAt      >  2:773204/1‑144 (MQ=255)                                                                                                                                                        |                                                                                                                                                      ACTCGTAGGCCTGATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCC‑TTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCG‑CAACAAAA‑‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357730‑358025

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑