Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	42.3%	84.0 / 16.2	54	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (24/6);  new base C (0/22);  total (24/30)
Fisher's exact test for biased strand distribution p-value = 1.60e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCG  >  NC_000913/1376356‑1376654                                                                                                                                                       |                                                                                                                                                      gCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAacac                                                                                                                                                      >  1:306428/1‑151 (MQ=255)      ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACTGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACTCCCTc                                                                                                                                                  <  2:269661/150‑1 (MQ=255)      ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCg                                                                                                                                                 >  1:50386/1‑151 (MQ=255)       cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGc                                                                                                                                                <  1:305238/151‑1 (MQ=255)            aTGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATg                                                                                                                                           <  2:71557/151‑1 (MQ=255)              gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGc                                                                                                                                          <  2:620962/150‑1 (MQ=255)                 cTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccgc                                                                                                                                      >  1:633579/1‑151 (MQ=255)                       gcgTATCCTGGACGGCGACCGCAAAATGGTGATTGATTCCCTGCGTGTACTGGAACAGGTCTCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTAAAA‑CCGCTATAAAGATCATATGATCAACCCCCTCGCCGATGCccgccg                                                                                                                                    <  2:914793/147‑1 (MQ=255)                        cgTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTAc                                                                                                                                >  1:763948/1‑150 (MQ=255)                           aGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcg                                                                                                                            >  2:406173/1‑151 (MQ=255)                                    ggCGCCCGAAAAATGGTGAGTGTTTCCCTGCGCGTACTGAAAAAGGTCGCCGCGCGTCCGGAAACGGTGGTTTATCTCGAACCGTTAAC‑CCGTTACCAGAATAATATAATAACCCCCCTCCCCGATGCCCGCCGTTACATCGTCGaaaa                                                                                                                     <  1:765930/149‑1 (MQ=255)                                         cggCAAAAGGGTGAGTGATCCCCGGCGCGTCCGGGAACGGGCCGCCGCGCGTCCCGGAACCGTGGTTTTTCTCGACCGTTTAAA‑CCGTTACAAGGATAATAGAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGa                                                                                                                  <  2:297563/145‑1 (MQ=255)                                             aaaaGGGTGAGTGATTCCCTGCGCGTACTGAAACAGGCCCCCGCGCGTACCGGACCCGTGGTGTATCTCAAACCTTAAAC‑CCGCTATCAGGATAATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                              <  2:261491/147‑1 (MQ=255)                                              aaaTGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                          >  2:498755/1‑150 (MQ=255)                                              aaaTGGGGGTTGTTTCCTCGCGCGTCCGGAAAGGGGTCGCCGGGCGTCCCGGAACGGTGGTGTATCTCGACCCGTAAAC‑CCACTATCAGGAACATATGAACAACCCCCTCGCCGCGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACa                                                                                                         <  2:140614/151‑1 (MQ=255)                                                        tgtttCCCTGCGCTTTGTGGAAGGGGCCGCCGCGCGTACGGAAACGGGGTTGTATCTC‑AACCCTTAAACCCGTTATCAGTATAATATGATAACCCCCCTCCCGGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                                <  2:806781/147‑1 (MQ=255)                                                         gtttCCCTGCGCGTCCTGGAACGGGTCGCCGCGCGTACCGGACCCGGGGTGTATCCCGAACCGTTAAC‑CCGCTATCAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                                <  2:816008/147‑1 (MQ=255)                                                                tGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                        >  2:129220/1‑150 (MQ=255)                                                                 ggcggtatgggACCAGGTCGCCGCTCGCCCTGGACCCTTGGTGTTTCCCAAACCGCCAAC‑CCTCTATCAGGCTGTAAAGCGAAACCCCCCCGCAGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCgg                                                                                          <  2:707952/138‑1 (MQ=255)                                                                      tACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                  >  2:13916/1‑150 (MQ=255)                                                                         tGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                               >  2:98831/1‑150 (MQ=255)                                                                         tGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                               >  1:823982/1‑150 (MQ=255)                                                                          gaaaCAGTCCGCCGCGCGCCCCGAAACTGTTGT‑TATCCTCAACCCTTAAACCCGCTATCAGAAACAAATGATCACCACCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGa                                                                                       <  2:132315/139‑1 (MQ=255)                                                                                ggcccccgcGCGTCCCGGACCCGGGGTGTATCCCGAACTTTAAAC‑CCGCTAAGAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                          <  2:241484/143‑1 (MQ=255)                                                                                ggTCGCCGCGCGTCCCGGACCGGTGGTTTTTCTCCAACCGTTAAC‑CCGCTATCAGGTTAATATGACCACCTCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                                       <  1:772563/151‑1 (MQ=255)                                                                                 gTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                                       >  2:265846/1‑150 (MQ=255)                                                                                   cgccgcGCGTACCGGACCTGTGGTGTATCTCAACCCTTTAAC‑CCGCTATCAGGATAATATAATCAACCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATg                                                                          <  2:459580/145‑1 (MQ=255)                                                                                   cgccgcGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                                    >  1:169039/1‑151 (MQ=255)                                                                                     ccgcGCGTCCCGAACCGGTGGTGTATCTCCAACTTTAAAA‑CCGCTAACGGAATCATAGGACAACCCCCCTCCCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                   <  2:296990/150‑1 (MQ=255)                                                                                       gcgggTCCCGAAACGGGGGTCTATCTCGCCCCTTAAAC‑CCTCTTTAGGGATCATATGCTAAACACCTTGCCCGACCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                   <  1:827810/148‑1 (MQ=255)                                                                                       gcgcgTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                                  >  2:672806/1‑149 (MQ=255)                                                                                        cgcgTCCGGGACCCGTGGTTTATCCCGACCCGTAAAA‑CCGCTATCAGGATCATATGACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaa                                                                 <  1:914683/149‑1 (MQ=255)                                                                                          cgTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                               >  2:823744/1‑149 (MQ=255)                                                                                               cGGACCGGTGGTTTCTCCCAAACCGTTAAC‑CCTTTATAAGTAAAATATGACAAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATa                                                          <  2:508624/149‑1 (MQ=255)                                                                                               cGGAACGGTGTTGTATCTCGACCCTTAAAC‑CCCCTATCAGGATCATATGACAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAagaaga                                                            <  1:232295/147‑1 (MQ=255)                                                                                               cGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                        >  1:512918/1‑151 (MQ=255)                                                                                                ggACCCGTGGTTTATCTCGACCCTTTAAC‑CCGCTATCAGAATAATAGGAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                         <  1:707044/149‑1 (MQ=255)                                                                                                ggAACCGTGGTGTATCTCGAACCTTTAAC‑CCGCTATCAGGATAATATGATCAACCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                           <  2:422250/147‑1 (MQ=255)                                                                                                  acccGTGGTTTATCTCAACCCTTTAAC‑CCTCTATCAGAATCATATAATCACCCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAGCCt                                                      <  1:270000/148‑1 (MQ=255)                                                                                                   aCCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                    >  1:482074/1‑151 (MQ=255)                                                                                                    ccGTGGTGTATCCCGACCCTTTAAC‑CCGCTATCAGGATAATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                     <  2:876439/149‑1 (MQ=255)                                                                                                       tggttTACCCCGACCCTTAAAC‑CCGTTATAAGGATAATAGGACCAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCt                                                      <  1:809928/145‑1 (MQ=255)                                                                                                          ttttccccaacccGTAAAC‑CCGTTTTCAGAATAATAGAAACACCCCCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                     <  2:512797/132‑1 (MQ=255)                                                                                                            tATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgcgc                                           >  1:886162/1‑151 (MQ=255)                                                                                                                 cGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCAt                                      >  1:872171/1‑151 (MQ=255)                                                                                                                  caaCCCTTAAACCCGCTATCAGGATCATATGACCAACCCCCTCCCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGc                                        <  1:226820/148‑1 (MQ=255)                                                                                                                   aaCCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                                     >  1:35847/1‑150 (MQ=255)                                                                                                                    aCCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                                   >  2:184620/1‑151 (MQ=255)                                                                                                                    aCCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                                   >  1:134128/1‑151 (MQ=255)                                                                                                                          aaa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                             >  2:362200/1‑151 (MQ=255)                                                                                                                           aacccGCTATAAGAATAATATAACCACCCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcg                              <  2:624444/147‑1 (MQ=255)                                                                                                                                   aacAGGATCATATGAACAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCt                        <  1:702504/146‑1 (MQ=255)                                                                                                                                      aGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg                  >  2:686908/1‑151 (MQ=255)                                                                                                                                            atatGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgt            >  1:99645/1‑151 (MQ=255)                                                                                                                                             tatGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgtg           >  1:847895/1‑151 (MQ=255)                                                                                                                                                      cacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCg  >  2:817716/1‑151 (MQ=255)                                                                                                                                                       |                                                                                                                                                      GCTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCG  >  NC_000913/1376356‑1376654

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: ‑