Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	357,890	0	C	A	50.0%	10.9 / 26.5	36	L267F (TTG→TTT)	cynR	transcriptional activator of cyn operon; autorepressor
Reads supporting (aligned to +/- strand):  ref base C (13/5);  new base A (0/18);  total (13/23)
Fisher's exact test for biased strand distribution p-value = 7.42e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.01e-01

GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357742‑358023                                                                                                                                                      |                                                                                                                                         gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa                                                                                                                                        >  2:1437007/1‑151 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa                                                                                                                                        >  2:40260/1‑151 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa                                                                                                                                        >  1:733556/1‑151 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGc‑aacaa                                                                                                                                        >  2:370716/1‑151 (MQ=255) gATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGCGATTCACTTTCTCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGGCTGCCCGCTATTTTTCCGCCGc‑aacaa                                                                                                                                        >  1:1451310/1‑151 (MQ=18)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑ccg                                                                                                                                  >  2:1320878/1‑151 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑ccg                                                                                                                                  >  1:177924/1‑151 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑ccg                                                                                                                                  >  2:42392/1‑151 (MQ=255)      gCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑ccg                                                                                                                                  >  2:580522/1‑151 (MQ=255)              cATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTtct                                                                                                                           >  2:803016/1‑150 (MQ=255)                    gcattccccgCCGAAGCCCTGTGTCGGGGCCTCCCGTGTTTCTTTCCCCCAAACACCCGCGCATTTACCCAACCCCATGTGAAAAAATCCCTTCGGGGCGGCTGTCTCCCAGCTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCag                                                                                                                     <  2:860274/141‑1 (MQ=255)                      aaTTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                  >  2:1107904/1‑151 (MQ=255)                      aaTCCCAGCCACAGACTTGTGCCAGCGGCTCCGGTGTTTAATTCCCGCCAACACCCGGGCATTTACCAAACGCAATGTGAAAAAAGGCTTGCGGGGGGGCTGTCTGCCGGTTTTTTTCCCGCCGA‑AAAAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                  <  2:247343/151‑1 (MQ=255)                                     ccggtgtCGGCGCCTACCGTTATTCATTCCCCCCAACACCCGCGCTTTTACCCAACCCAATTGACAAAAAGGCCTCCGGGGCGGCTGTCTGCCAGCTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAgaga                                                                                                  <  2:316645/148‑1 (MQ=255)                                     ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑ggggggcagga                                                                                                  >  2:341874/1‑144 (MQ=255)                                     ccTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGgagaga                                                                                                  >  1:409506/1‑151 (MQ=255)                                                 gCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGGAGAGaaaaaaagttaaa                                                                                      >  2:56729/1‑141 (MQ=255)                                                     ccGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGGCGGAGAAAAAACTTTTAAGccg                                                                                  >  2:1411492/1‑150 (MQ=25)                                                          tttatttccccccAACACCCGCGCTTTTACCCAACGCATTGTGCAAAATTCCCTCGGCGGGGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtg                                                                            <  2:59354/140‑1 (MQ=255)                                                          aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCagtag                                                                                                                  >  1:456725/1‑115 (MQ=255)                                                          aTTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGCGGGGGCAAGGAAAAAAGC‑TTTAAAcccccc                                                                               >  2:1216438/1‑146 (MQ=25)                                                             ctttccccccAACACCCGCCATTTTACCCACCGCCATGTGAAAAAAGGCCTCCGGGGCGGCTGTCTGCAGGTTTTTTTCCCGCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCAtgttg                                                                         <  2:506918/143‑1 (MQ=255)                                                                     ccaccacccgccattttACCCACCCCCATGTGAAAAAATGCCTCCGGGGCGGCTGTCGGCCAGTTTTTTTCCCCCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCaa                                                                 <  2:603761/137‑1 (MQ=255)                                                                                   ttccccaaaCGCCATGACAAAAAATGCCTCCCGGGCGGCTGTCTGCCAGTTATTTTGCCGCCAC‑AACAAAG‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAAc                                                   <  1:436371/144‑1 (MQ=255)                                                                                     tccccACCGCCATGTAAAAAAATCCCTCCGGGGCGGCTGTCGCCCGGTTTTTTTCCCGCCGC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                 <  1:628366/148‑1 (MQ=255)                                                                                     tacccacccccATGTAAAAAAATGCCTTCGCGGCGTCTGTCGGCCGGTTTTTTTCCCGCCCC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACaa                                                 <  2:1039680/142‑1 (MQ=255)                                                                                      aTCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGAC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAt                                                >  2:77610/1‑151 (MQ=255)                                                                                       tccacccccaggaaaaaaaaTGCTTTCGGGGGGCCTGTCTGCCACCTTTTTTCCCGCGGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtg                                               <  2:1195770/136‑1 (MQ=255)                                                                                        caaccccaaggtcaaaaaaTCTCTGCGCGCCGGCTTTCTCCCGGCTATTTTCCCCCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGG‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAAtgt                                              <  2:1010273/137‑1 (MQ=255)                                                                                           ccgccttggccAAAAATCCTTTCGGGGCGGTTTTCTGCCAGTTTTTTTCCCCCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGa                                           <  2:1293712/141‑1 (MQ=255)                                                                                              ctatttgaaaaaaTGCCTCCGCGGCGGCTCTCTGCAATTTTTTTTCCCCCCCA‑AACAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGaaa                                         <  1:1175276/142‑1 (MQ=255)                                                                                                 tgtgAAAAAATGCTTCCGCGGCGGCTGTCGGCCAGTTTTTTTCCCGCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGa                                     <  2:1248124/151‑1 (MQ=255)                                                                                                        aagcgcctcgcgggcggcGGTCGACCAGCTATTTCCCGGCGGC‑AACAAAT‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTgcgg                              <  1:1104141/139‑1 (MQ=255)                                                                                                              tttCGGGGCGGCTGTC‑GCCAAGTTTTTTTCCCCCCC‑AAAAAAACCCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATc                        <  2:870811/150‑1 (MQ=255)                                                                                                                         ttttccgCCTGCTGTTTTCCCGACAC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc             <  1:811115/145‑1 (MQ=255)                                                                                                                         ctttccgCCAGTTTTTTTCCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc             <  2:1418314/145‑1 (MQ=255)                                                                                                                         ctgtcggccgttttttttcCCGCCAC‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc             <  1:374383/137‑1 (MQ=255)                                                                                                                         cTGTCTCCCGGTTTTTTTCCCCCCGA‑AAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc             <  2:1225284/151‑1 (MQ=255)                                                                                                                         cTGTCGGCCGGTTTTTTTCCCGCCGC‑AAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAAc             <  2:914100/151‑1 (MQ=255)                                                                                                                              tcccAGCTTTTTTCCCCCCGC‑AAAAAAC‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCgcgc        <  2:14813/149‑1 (MQ=255)                                                                                                                                     tttttttCCCCCCCAAAAAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTg  <  2:1437514/149‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                         GATAAGCGTAGCGCATCAGGCAATTCCAGCCGCAGACCTGTGTCAGCGGCTACCGTGATTCATTTCCGCCAACAACCGCGCATTTATCCAACGCCATGTGCAAAAATGCCTTCGCGGCGGCTGTCTGCCAGCTATTTTTCCGCCGC‑AACAAAA‑CCGCCGTTCTCTCCAGTAGTGGC‑GGGGCAAGAGAAATAGC‑TTTAAGCCCGTCATGTTGTGTGGCAATCGCTGCTGGTAACAATGTGGAAAGGGAAGTGCGGCGAATCAGCTCCAGAACCGCGCTAATTG  >  NC_000913/357742‑358023

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: ‑