Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	46.7%	58.9 / 17.4	45	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (15/9);  new base C (0/21);  total (15/30)
Fisher's exact test for biased strand distribution p-value = 3.95e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGC  >  NC_000913/1376357‑1376646                                                                                                                                                      |                                                                                                                                              cTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAacac                                                                                                                                              <  2:175313/150‑1 (MQ=255)    aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                          >  2:921957/1‑151 (MQ=255)     ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                          <  2:347574/150‑1 (MQ=255)     ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                          <  1:625999/150‑1 (MQ=255)     ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCg                                                                                                                                         <  2:340162/151‑1 (MQ=255)         cgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGa                                                                                                                                     <  1:737650/151‑1 (MQ=255)           aTGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATg                                                                                                                                   <  2:38763/151‑1 (MQ=255)            tGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGc                                                                                                                                  >  2:615468/1‑151 (MQ=255)             gACCTCCGCGCGTAGCCTGGACGGCGACCGCAAAATTGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATAAACACCCTCGCCGATGc                                                                                                                                  <  1:734336/150‑1 (MQ=255)              aCCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGccc                                                                                                                                >  2:31216/1‑151 (MQ=255)                  cgccgcGTAGCCTGGACGGCGACCGCAAAATGGGGAGTGTTTCCCTTGGCGTCCTGGAACAGTTCGCCGCGCGTACCGGACCCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccgcc                                                                                                                             <  1:632443/150‑1 (MQ=255)                               ggccGGCGCCCGCAAAAGGGTGAGTGATTCCCTGCGCGTACTGAAACGGGTCGCCGCGCGTACCGAAACCGTGGTGTATCCCGAACCGTAAAA‑CCGCTATCAGGATCATATGACAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGaa                                                                                                               <  2:134998/148‑1 (MQ=255)                                      gACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCACCGTTACATCGTCGAAAACGATc                                                                                                        <  1:74022/151‑1 (MQ=255)                                       accgaaaggtGGTGTGTGACCCCCGGCGCGTCCTGAAACACGTCGCCGCGCGTCCCGGACCGGTTGTGTACCTCGCCCCGTTAAC‑CCGATTTGAGGACCGTATGATAAACACCCCCCCCGTTCGCCGCCGTTACATCGTCGAAAAc                                                                                                            <  2:379866/137‑1 (MQ=255)                                             aaaGGGGGAGTTATTCCCTGTGCTTACTGGCACAGGTCGCCGCGCGTACGGGAACCGTGTTTTACCCCGACCCTTTAAC‑CCGCTTTCAGGATAATATAAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACa                                                                                                 <  1:826969/151‑1 (MQ=255)                                                    gagtgaTCCCCTGCGCTTACGGAAACGGGTCCCCGCGCGTCCCGGAACCGTGGTTTATCTCGACCCTTAAAA‑CCGCTATAAGAATCATAAAACCACCCCCCCCGCCTATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACa                                                                                           <  1:719753/150‑1 (MQ=255)                                                          ttCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                    >  2:854566/1‑151 (MQ=255)                                                            cccGGCGGGTTCTGGAACGGGTCGCCGCGCGTACCGGAACGGTGGTGTATCTCAAACCGTTAAC‑CCGCTATCAGGATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                     <  2:1043824/148‑1 (MQ=255)                                                            cccGGCGCTTACGGGAACGGGTCGCCGCGCGTCCCGAACCGGTGGTGTATCTCGACCCGTAAAC‑CCGTTATAAGAATAATATAATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCg                                                                                   <  2:973949/150‑1 (MQ=255)                                                                gcggttacggaaaCGGGCCGCCGCGCTTCCCGGACCGGTGGTTTATCCCGACCCGTAAAC‑CCGCTATCAGAATAATATAAACACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                <  1:610227/138‑1 (MQ=255)                                                                    ttACTGAACCAGGCCCCCGCGCGTCCCGGACCCGTGGTGTCCCCCCACCCGTAAAC‑CCGCTAACAGAATCATATAACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                                 <  1:389899/143‑1 (MQ=255)                                                                    gTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                          >  1:446855/1‑151 (MQ=255)                                                                      acggaaccAGGTCGCCGCGCGTCCCGGACCGGTGGTGTTTC‑CCAACCCTTAAACCCGCTATCGGGAAAATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                <  1:326242/136‑1 (MQ=255)                                                                                  cgccgcGCGTCCCGGACCCGTGGTTTATCTCGAACCGTAAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                            <  2:634394/151‑1 (MQ=255)                                                                                   gccgcGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                           >  1:657028/1‑151 (MQ=255)                                                                                            aCCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                   >  1:899160/1‑150 (MQ=255)                                                                                             ccgaacccGTGGTTTATCTCGAACCGTTAAC‑CCGTTACCAGAATCATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                 <  1:537751/145‑1 (MQ=255)                                                                                               ggAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                               >  2:890527/1‑151 (MQ=255)                                                                                                 accggtggtgTACCAC‑AACCGTTAAACCCGCCATCAGAATTATATGATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaa                                                         <  2:616494/135‑1 (MQ=255)                                                                                                   cggggttgtATCTCGACCCTTTAAA‑CCGTTATCAGAATCATATAATCACCCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                            <  1:831956/144‑1 (MQ=255)                                                                                                   ccGTGGTTTATCCCGACCCGTTAAC‑CCCCTATCAGGATAATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                             <  1:261344/149‑1 (MQ=255)                                                                                                     gtggtgTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                         >  2:508834/1‑151 (MQ=255)                                                                                                       ggtgTATCTCAAACCTTAAAC‑CCGTTATCAGAATCATATAAAAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                            <  2:926501/146‑1 (MQ=255)                                                                                                          gtATCTCGACCCTTTAAC‑CCGCTACCAGGATCATATGATCAACCCCCTCGCCTATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAgg                                      <  2:353758/149‑1 (MQ=255)                                                                                                                  aaCCTTAAAC‑CCCCTATCAGAATCATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                             <  2:924785/150‑1 (MQ=255)                                                                                                                  aaCCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                             >  1:413463/1‑150 (MQ=255)                                                                                                                   aCCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                           >  1:357027/1‑151 (MQ=255)                                                                                                                    ccttaaaa‑CCCCGAACAGAATAATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGc                                <  1:714875/140‑1 (MQ=255)                                                                                                                          aacccGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                     <  2:191672/148‑1 (MQ=255)                                                                                                                          aa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                    >  2:837791/1‑151 (MQ=255)                                                                                                                                   tCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc            >  2:338951/1‑151 (MQ=255)                                                                                                                                    cAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg           >  1:914894/1‑151 (MQ=255)                                                                                                                                           atatGACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAt      <  2:692286/149‑1 (MQ=255)                                                                                                                                             atGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGc  >  2:601315/1‑151 (MQ=255)                                                                                                                                             agtaacAACCCCCTCGCCGTTCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg     <  2:291254/143‑1 (MQ=255)                                                                                                                                              tGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCt             <  2:459156/139‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                              CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGC  >  NC_000913/1376357‑1376646

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑