Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	47.7%	37.2 / 27.6	44	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (17/6);  new base C (0/21);  total (17/27)
Fisher's exact test for biased strand distribution p-value = 1.56e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCAT  >  NC_000913/1376359‑1376648                                                                                                                                                    |                                                                                                                                                tACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCt                                                                                                                                             >  2:668306/1‑151 (MQ=255)   ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCg                                                                                                                                           <  1:56955/151‑1 (MQ=255)    cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGc                                                                                                                                          <  2:487348/151‑1 (MQ=255)                             ggcggcggaccaaaaaaTGGGGAGTGCTCCCCGGCGCGGCCGGGACGGGGTCGCCGCGTGCCGCGGAACGGGGGTTTATCCCAACCCGTAAAC‑CCGTTATCGGAAAAATATGACAAACCCCCCGGCCGATGCCCGCCGTTACAtc                                                                                                                       <  1:769060/132‑1 (MQ=255)                              gACGGCGACCGAAAAAGGGTGAGTGATCCCCGGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGACCGGTGGTGTATCTCGAACCGTTAAC‑CCGCTATCAGGATCATATAACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGaaa                                                                                                                <  2:14346/151‑1 (MQ=255)                                 ggCGCCCGAAAAATGGTGAGTGTTTCCCTGCGCGTACTGAAACAGGTCGCCGCGCGTCCCGAACCCGTGGTTTATCTCAAACCTTTAAA‑CCGCTATCAGGATCATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACg                                                                                                             <  2:641717/151‑1 (MQ=255)                                     aCCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCt                                                                                                         >  1:398288/1‑151 (MQ=255)                                      ccGAAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGACCCGTGGTGTATCTC‑AACCCTTAAACCCGCTATCAGGATAATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                        <  2:654016/151‑1 (MQ=255)                                         aaaaaGGGGGAGTGTTTCCCGGCGCTTACTGAAACGGGCCGCCGCGCGTCCCGGACCGGGGGTGTATCTCGACCCGTAAAC‑CCGTTAAAAGGATCATATGAACACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                      <  1:770868/149‑1 (MQ=255)                                          aaaaTGGTGAGTGATTCCCTGCGCGTACTGGAACGGGTCCCCGCGCGTCCCGGACCCGTGTTTTATCTCGAACCGTTAAC‑CCGCTATCAGGATCATATAATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                    <  2:823728/151‑1 (MQ=255)                                          aaaaGGGTGAGTGTTTCCCTGCGCGTACTGAAACAGGCCGCCGCGCGCCCCGAAACCGTGGTGTCCCTCAAACTTAAAAC‑CCGCTATCGGGATAAAATGACAAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGaaa                                                                                                                <  1:275014/139‑1 (MQ=255)                                           aaaTGGTGGGTGTTTCCCTGCGCGTACGAAACCAGGTCGCCGCGCGTCCCGAACCCGGGTTGTATCTCGACCATTAAAA‑CCGCTATCAGGATAATAAGCACACCACCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                      <  1:370559/148‑1 (MQ=255)                                           aaaGGGGGAGTGATCCCCTGCGCGTACTGGAACGGGCCGCCGCGCGTACCGAAACGGTGGTGTATCTCAAACCTTAAAC‑CCGCTACCAGAATAATATGACCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACa                                                                                                   <  2:598407/151‑1 (MQ=255)                                               ggggagttttccccTGCGCGTACTGGAACAGGTCGCCGCGCTTACGGGAACGGTGGTGTATCTGGAACCTTTAAC‑CCGTTATCAGAATAATTTGACAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATg                                                                                                 <  1:573196/138‑1 (MQ=255)                                                gtgagtgtTTCCCGGCGCTTACTGGAACAGGTCCCCGCGCGTCCGGGAACGGTGTTGTATCTCAAACCTTAAAC‑CCGTTATCAGAATAATATAATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                              <  2:674933/151‑1 (MQ=255)                                                gtgagtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                              >  2:273979/1‑151 (MQ=255)                                                       aTTCCCGGCGCGTACGGGAAGGGGCCGCCGCGCGTACCGAAACCGTGGTGTATCCAGAACCGTAAAC‑CCCTTATCAGATTAATATGATCAACCCCCTCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                         <  1:439134/149‑1 (MQ=255)                                                        ttCCCGGCGCTTACGGAAACAGGTCGCCGCGCGTCCCGGACCCGTGGTGTACCCCGACCCGTAAAC‑CCGCTATCAGGATCATATGACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                         <  2:339809/148‑1 (MQ=255)                                                        tccccGGCTCGTACGGGAACAGGTCGCCGCGCGTCCCGAACCCGTGGTGTATCTCGACCCTTTAAC‑CCTTTATAAGAATAATAAGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTAt                                                                                       <  1:375888/148‑1 (MQ=255)                                                               cgcgTACGGGAAAAGGTCGCGGCGCGTCCGGGACCGGGGGGGTATCTC‑AACCCTTAAACCCGCTTACGGAATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                                   <  2:257158/147‑1 (MQ=255)                                                                gcgTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                  <  2:577296/147‑1 (MQ=255)                                                                        gAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                       >  1:227186/1‑150 (MQ=255)                                                                         aaCGGGCCGCCGCGCGTCCCGAACCGGTGGTGTTTCCCGACCCTTAAAC‑CCGCTATAGGAATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACAt                                                                     <  1:342875/151‑1 (MQ=255)                                                                          acgggTCCCCGCGCGTACCGGAACGGTGTTTTATCCCGACCCGTTAAC‑CCGCTATCAGGATAATATGAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcaca                                                                      <  2:196214/146‑1 (MQ=255)                                                                                       cgTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                         >  1:181410/1‑149 (MQ=255)                                                                                           ccGGACCCGTGGTTTATCTCGACCCGTTAAC‑CCTCTATCAGGATAATATAACAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATa                                                    <  2:510248/150‑1 (MQ=255)                                                                                            cGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                   >  1:778220/1‑150 (MQ=255)                                                                                            cGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                  >  2:822368/1‑151 (MQ=255)                                                                                             ggAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                 >  2:688321/1‑151 (MQ=255)                                                                                                     ggtgTACCCCGACCCTTAAAC‑CCTCTACAAGAATAATATGAACAACACCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcg                                            <  1:761105/148‑1 (MQ=255)                                                                                                             tcGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGc                                  >  1:309963/1‑150 (MQ=255)                                                                                                                 aCCTTTAAACCCTCTATCAGGATCATATGATCAACACCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGa                              <  2:688173/151‑1 (MQ=255)                                                                                                                 aCCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                             >  1:147783/1‑151 (MQ=255)                                                                                                                     ttAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                         >  1:582103/1‑151 (MQ=255)                                                                                                                       aaa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgc                       >  2:456429/1‑151 (MQ=255)                                                                                                                        aacccGCTATCAGGATCATATGATCACCACCCTCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACaa                           <  2:762813/144‑1 (MQ=255)                                                                                                                        aacccGCTACCAGAATCATATAACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAcc                         <  2:827491/146‑1 (MQ=255)                                                                                                                         a‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                      >  1:126723/1‑150 (MQ=255)                                                                                                                                   aGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg            >  1:231219/1‑151 (MQ=255)                                                                                                                                           ataaTCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAt        <  2:209828/144‑1 (MQ=255)                                                                                                                                            taaccAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCa         <  1:639718/141‑1 (MQ=255)                                                                                                                                            tGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGc    >  2:94169/1‑150 (MQ=255)                                                                                                                                              aTCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCat  >  2:567954/1‑150 (MQ=255)                                                                                                                                               tCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCat  >  2:755899/1‑149 (MQ=255)                                                                                                                                                    |                                                                                                                                                TACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACCGTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCAT  >  NC_000913/1376359‑1376648

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: ‑