Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	46.4%	75.4 / 16.5	56	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (22/8);  new base C (0/26);  total (22/34)
Fisher's exact test for biased strand distribution p-value = 3.66e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAT  >  NC_000913/1376358‑1376642                                                                                                                                                      |                                                                                                                                          ttACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACAccc                                                                                                                                        >  1:35341/1‑151 (MQ=255)    ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCt                                                                                                                                       <  1:882429/149‑1 (MQ=255)    ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                      <  1:731225/150‑1 (MQ=255)       ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                  >  1:483371/1‑151 (MQ=255)       ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                  <  2:365139/151‑1 (MQ=255)            gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGGGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                             >  2:240376/1‑151 (MQ=255)              ccTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTTGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccg                                                                                                                           <  1:612229/151‑1 (MQ=255)                   ccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGtt                                                                                                                      >  1:518064/1‑151 (MQ=255)                             tGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                             >  2:587097/1‑150 (MQ=255)                              ggcgggCGACCGAAAAAGGGTGGGTGTTCCCCTGCGCGTACGGGAACAGGTCGCCGCGCGTCCGGGAA‑CCGGGGTGTATCTCGACCCGTAAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                             <  2:321038/145‑1 (MQ=255)                                aCGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGaaa                                                                                                          >  2:358051/1‑150 (MQ=255)                                 cGGCGCCCGAAAAAGGGTGAGTGTTCCCCTGCGCGTACTGAAACGGGTCGCCGCGCGTACCGAAC‑CGGTGGTGTATCTCGACCCGTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGaaaa                                                                                                         <  2:181519/150‑1 (MQ=255)                                  ggcgcccaaaaaaGGGTGATTTTTCCCCTGCGCGTACGGGACCGGGTCGCCGGGCTTCCCGAAC‑CGGTGTTTTTCCTCAAACCTTTAAC‑CCGCTAACGGGTTCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                             <  1:861644/136‑1 (MQ=255)                                       ccGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                  >  2:181088/1‑151 (MQ=255)                                       ccGAAAAAGGGGGAGTGATTCCCTGCGCGTCCGGAAACAGTTCGCCGCGCGTACGGAAC‑CCGTGGTGTATCCCG‑ACCGTTAAACCCGCTACCAGGATAATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                     <  2:133261/148‑1 (MQ=255)                                        cGCAAAAGGGTGAGTGATTCCCGGCGCGTACGGAACCAGGTCGCGGGGCGTACCGGAA‑CGGGGTTTTATCTCGACCCGTAAAC‑CCGCTATAGGGATCATATAACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTa                                                                                                 <  2:766773/151‑1 (MQ=255)                                                ggTGAGTGATTCCCTGCGCTTACTGGAACAGGTCGCCGCGCGTACCGAAC‑CCGTGGTTTATCTCGACCCTTTAAC‑CCGCTATCAGGATCATATGAACAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTa                                                                                         <  2:171022/151‑1 (MQ=255)                                                  tgagtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                        >  1:109968/1‑150 (MQ=255)                                                   gggtgcTTCCCTGCGCGTCCTGGAACGGGTCCCCGGGCGTCCCGGAC‑CGGTGGTGAACCCCAACCCGTCAAC‑CCCCTAACAGAATCATATCATCAACCCCCCCGCCGTGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                        <  1:347311/147‑1 (MQ=255)                                                   gagtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                        >  2:684995/1‑149 (MQ=255)                                                     gtgaTTCCCGGCGCTTACTGAAACGGGTCGCCGCGCTTACCGAAC‑CCGTGGTGTATCTCGACCCTTTAAC‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGa                                                                                     <  2:609336/150‑1 (MQ=255)                                                        aTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                 >  1:524715/1‑151 (MQ=255)                                                         ttCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                >  1:139736/1‑151 (MQ=255)                                                         tccccGGCGCTTACGGAAACAGGCCCCCGCGCGCCCGGGAC‑CGGTGGTGTACCCCAACCCGTAAAC‑CCGCTACAAGGATAATATAAAAAACCCCCTCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAg                                                                                      <  1:684950/143‑1 (MQ=255)                                                           cccTGCGCTTACTGAAACAGGTCGCCGCGCGTCCCGAAC‑CCGTGTTGTATCTCGACCCTTAAAC‑CCTCTATCAGGATAATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCgg                                                                              <  2:35886/151‑1 (MQ=255)                                                           cccTGCGCGTACTGGAACAGGTCGCCGGGCGTACCGGAC‑CGGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCgg                                                                              <  2:732789/151‑1 (MQ=255)                                                           cccGGCGCTTACGGAAACAGGTCCCCGCGCGTCCGGGAC‑CGGTGGTGTATCTCGACCCGTAAAC‑CCGCTATAAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                   <  2:585126/146‑1 (MQ=255)                                                           cccGGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGAA‑CGGTGGTGTATCTCGACCCGTTAAC‑CCGCTATCAGGATCATATGACCAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCg                                                                               <  2:859820/150‑1 (MQ=255)                                                           cccGGCGCGTACGGGAGCGGCTGCCCGCGCCTACAGGAA‑CGGGGTTGAGTCTCGACCCGTAAAC‑CCGTTACCAGGATCAAATGATAACCCCCCCCGCCGCTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                <  2:586879/149‑1 (MQ=255)                                                             cTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                            >  2:34669/1‑151 (MQ=255)                                                                cgtgTATTGGAACAGGTCGACGCGCG‑CCCGAAACCCGGGGTGTCTCCAGAACCGTAAAC‑CCGCTATCAGTATCATATGACTAACCCCCCGGCCTAAGGCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                 <  2:96477/140‑1 (MQ=255)                                                                       gggAACGGGTCGCCGCGCGTCCCGGAA‑CGGGGGTGT‑CCCCCAACCTTTAAACCCGCTACCAGAATAATAAGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                        <  1:825973/144‑1 (MQ=255)                                                                        ggAACGGGTCGCCGCGCGTCCCGGAC‑CCGTGGTGTATCTCGACCCTTAAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                       <  2:177935/145‑1 (MQ=255)                                                                        gaaaCAGGCCGCCGCGCGTACCGAAA‑CGGTGGTGTATCCCGAACCTTTAAC‑CCGCATTCAGAATCATATAATAACCACCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTa                                                                     <  1:796298/145‑1 (MQ=255)                                                                         gAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                 >  2:191063/1‑150 (MQ=255)                                                                          aaCGGGCCGCCGCGCGTACCGGAC‑CCGTGGTTTATCTCGACCCTTAAAA‑CCGCTATCAGGATAATATAATCACCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATca                                                                  <  1:157275/148‑1 (MQ=255)                                                                          aaCAGGTCGCCGCGCGTCCCGGAC‑CCGTGGTGTATCTCGACCCGTTAAC‑CCGCTATCAGGATCATATGATCAACCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                        <  2:796386/142‑1 (MQ=255)                                                                              ggTCGCCGCGCGTCCCGGAC‑CCGTGGTGTATCTCGACCCTTAAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                           <  2:415197/151‑1 (MQ=255)                                                                              ggTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                           >  1:837914/1‑151 (MQ=255)                                                                              ggTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                           >  1:272332/1‑151 (MQ=255)                                                                                ccgccgcGCGCCCCGGAC‑CCGTGCGGTATCGCGACCCGTTAAC‑CCTCTATCAGGATAATAGGACAAACCCCCCCGCGGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATca                                                                  <  1:675757/141‑1 (MQ=255)                                                                                             ccgaacccGTGGTTTTCCTCAACCTGTAAAC‑CCGGTAACAGTATCATAGAACCAACACCCCCGCCGACCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                               <  2:154247/143‑1 (MQ=255)                                                                                              ggAA‑CGGTGGTGTATCTCGACCCGTAAAA‑CCGCTATCAGGATAATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                           <  2:623542/151‑1 (MQ=255)                                                                                               gaacccGTGGTTTATC‑CCAACCTTTAAACCCGTTATAAGAATAATATAATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATa                                              <  1:360497/144‑1 (MQ=255)                                                                                                      gtgttttctcccaaCCCTTAAACCCGCTAAAAGAATAATATAACAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcg                                      <  1:519138/138‑1 (MQ=255)                                                                                                       ggtgTTTCTCAAACCTTAAAA‑CCGCTATAAGTATCATATGAAAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCa                                    <  2:130217/150‑1 (MQ=255)                                                                                                                  aaCCTTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgc                                 <  2:604864/142‑1 (MQ=255)                                                                                                                     cGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACa                      >  2:564399/1‑150 (MQ=255)                                                                                                                       ttAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                   >  2:188940/1‑151 (MQ=255)                                                                                                                         aaa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                 >  1:264829/1‑151 (MQ=255)                                                                                                                         aaa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGACGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcg                  >  1:183435/1‑150 (MQ=255)                                                                                                                          aa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCATGCGCTGCATGACAACcgcg                >  2:802160/1‑151 (MQ=255)                                                                                                                                  aTCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGc          >  2:88475/1‑150 (MQ=255)                                                                                                                                  aTCAGGATAATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGc          <  2:241649/150‑1 (MQ=255)                                                                                                                                        aTCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTc    >  2:440591/1‑150 (MQ=255)                                                                                                                                             atGAACAACCCCCCCGCCGAGTCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAt  <  1:419601/147‑1 (MQ=255)                                                                                                                                                      |                                                                                                                                          TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAT  >  NC_000913/1376358‑1376642

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑