Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	52.5%	27.5 / 65.3	40	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (14/5);  new base A (0/21);  total (14/26)
Fisher's exact test for biased strand distribution p-value = 5.01e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.16e-07

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357742‑358025                                                                                                                                                      |                                                                                                                                        gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGcaacaa                                                                                                                                       <  1:846815/151‑1 (MQ=255)     aGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                   >  2:298523/1‑151 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCGGACCTGTGTCAGCGGCTACCGTGATTCATTCCCGCCAACACCCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAcc                                                                                                                                   <  2:440818/150‑1 (MQ=255)       cGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgc                                                                                                                                 <  1:642999/151‑1 (MQ=255)        gTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAAccgcc                                                                                                                                <  1:805163/151‑1 (MQ=255)            cgcATCAGGCAATTCCAGCCGCAGCCCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAACATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtc                                                                                                                            >  2:244903/1‑151 (MQ=255)             gcATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTtct                                                                                                                           >  1:67559/1‑151 (MQ=255)                 cAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                       >  2:1005729/1‑151 (MQ=255)                  aGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTcc                                                                                                                       >  1:998194/1‑150 (MQ=255)                      aaTTCCGGCCGAAGCCTGGTGTCGGGGCCTCCCGTGATTCATTCCCGCCAACACCCGCCCTTTTACCCAACGCCATGTGAAAAAATGCTT‑CCGGGGCGGTTGTCGCCCAGTTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCagta                                                                                                                   <  1:855177/150‑1 (MQ=255)                         tCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                               >  1:1003353/1‑151 (MQ=255)                           cAGCCGCATACTTGTGACGGCGGCCACGGTGATTCACTCCCCCCCCCCCCCCCCCTTTTTCCCACCGCCGTGTGAAAAAATGCCT‑CCGGGGCGCCTGTCTGAAAGTTTTTTTCCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCg                                                                                                             <  2:129435/151‑1 (MQ=255)                              ccGCAGCCCTGTTCCGGCGGCACCCGTGATTCATTCCCCCAAACACCCGCGATTTTACCAACCCCCATGTGAAAAAAGGCCT‑CCGCGGCGGTTGTCTGCCAGTTATTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTgg                                                                                                               <  1:1089143/146‑1 (MQ=255)                                 cacctcTGTGTGCGCGGCTCCCGTGTTTCATCCCCGCAACCACCCGCCCTTTTACCCAGCGCCAGTTACAAAACTCCCT‑TCGGGGCGGCTGTCCGCCAGCTATTTTCCCGCCGAAAAAAAGCCGCCGTTCTCTCCAGTAGTGGCGGGGCa                                                                                                        <  2:45466/145‑1 (MQ=255)                                 cAGACCTGTGTAAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTg                                                                                                                >  2:279848/1‑142 (MQ=255)                                  aGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgg                                                                                                            >  2:591065/1‑145 (MQ=255)                                   gACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCgggg                                                                                                          >  1:242848/1‑146 (MQ=255)                                            cagcggcagcggTGATTCTTTCCCGCAAACAACCGCGATTTTCTCCAACCCGATTAAAAAAATTGCCT‑GGGGGCCGGCTGTCCCCCACATATTTCTCCGCGGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGaa                                                                                                  <  1:609647/145‑1 (MQ=255)                                              ggggttcccGTGTTTAATTCCCCCCAACCCCCGCTTTTTTACCAACCGCCATGTAAAAAAATGCCT‑TCGGGGGGGTTGCCTCCAGGCTTTTTTCCCGCGCCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                           <  1:569313/143‑1 (MQ=255)                                                ggCTCCCTTGCTTCCTTCCCGCCACAAACCGCGCTTTTACCCACCGCGATGTCAAAAAGTCCCT‑GGGGGGCGCCTTTCGCCCCGTTTTTTTCCCGCAGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCtt                                                                                           <  1:1051776/148‑1 (MQ=255)                                                    aCCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGaaaaaaaatttaatcc                                                                                    >  1:965765/1‑138 (MQ=25)                                                     ccGTTATTCTTTCCCCCAAACACCCCCGTTTTTACCCACCGCATTGTAAAAAAATCCCT‑TCGCGGGGGTTGTCGCCCATTTATTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCg                                                                                   <  1:550498/151‑1 (MQ=255)                                                     ccGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGATGAGaaaaaaaaataaactc                                                                                    >  1:782386/1‑137 (MQ=25)                                                        tGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAAAGAAAAAACGTTaaaaacccc                                                                                 >  1:664767/1‑143 (MQ=25)                                                               ttccccccAACACCCGCCTTTTTATCCACCCCAATGTAAAAAAATGCTT‑CCGGGGCGGCTGTCGGCGGTTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCAtgttgt                                                                          <  2:588868/144‑1 (MQ=255)                                                                           cccctgcttttACCCACCGCCTTG‑GCAAAAAATCCTCCCGCGGGGCCTGTCTGCGAGTTTTTTTTCCCCAGAAAAAAACCCGCCGTTCTCTCCAGTAGTGGCGGGTCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCgct                                                              <  2:84426/142‑1 (MQ=255)                                                                                        ccACCGCCATGTAAAAAAATGCCT‑GGGCGGCGGTTGTCTGCCACTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACa                                                    <  1:168390/147‑1 (MQ=255)                                                                                         caccGCCATGCCAAAAAGTCCCT‑CCGCGGCGGCTGTCTGCCGTTTTTTTTCCCGCCAAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                  <  2:566001/145‑1 (MQ=255)                                                                                            ccccaggtcaaaaaaTGCCT‑GCGCGGCGGCTGTCTCCCACTTTTTTTCCCCCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaa                                            <  1:1028207/141‑1 (MQ=255)                                                                                              ccATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGGAGAGAAAAAACTTTAAACCCGCCCCGTTTTGTGGGGAACGCTGCTGGGGACAATGTgg                                              >  1:178828/1‑147 (MQ=37)                                                                                              ccATGGGCAAAAATGCCT‑GCGGGGGGGCTGTCTCCCAGTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                             <  1:802090/148‑1 (MQ=255)                                                                                               cagttgCAAAACGCCCT‑CCGCGCCGGCTTCCTCCCACCTTTTTTCCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAg                                          <  2:67582/146‑1 (MQ=255)                                                                                                      aaaaaCCCCT‑CCGGGGCGTCTGTTTGCCCCCTTTTTTCCCGCCGCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgc                                  <  1:188517/151‑1 (MQ=255)                                                                                                            gCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGGCAGAGAAAAAAATTTTAACCCCCCAAGTTTTGTGGGGAAAGCTGCTGGTGAAAAAATGGGAAGGGGAGAggggcg                              >  1:2446/1‑149 (MQ=255)                                                                                                                   gcgccgGCTGTCTGCAATTTTTTTTCCCGCCACAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                          <  2:882975/147‑1 (MQ=255)                                                                                                                        ggcTTTCTCCCAGCTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                 <  1:398755/151‑1 (MQ=255)                                                                                                                           tttcggCCAGTTATTTTCCCCCCCAAACAAACCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGa                 <  2:769626/143‑1 (MQ=255)                                                                                                                               tccctctttttttcCCGCCCCAAAAAATCCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACcg             <  2:177056/139‑1 (MQ=255)                                                                                                                                 ccattttttttcCCGCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc               <  1:387998/137‑1 (MQ=255)                                                                                                                                 ccAGTTTTTTTCCCGCCGCAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTa        <  1:620066/151‑1 (MQ=255)                                                                                                                                        ttttcCCCCCGAAAAAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAg  <  2:1003029/150‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                        GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCT‑TCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGCAACAAAACCGCCGTTCTCTCCAGTAGTGGCGGGGCAAGAGAAATAGCTTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTGAG  >  NC_000913/357742‑358025

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: ‑