Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	51.1%	47.4 / 73.8	47	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (18/5);  new base C (0/24);  total (18/29)
Fisher's exact test for biased strand distribution p-value = 7.37e-09
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.02e-07

CCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCG  >  NC_000913/1376361‑1376654                                                                                                                                                     |                                                                                                                                                      ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTc                                                                                                                                                  <  1:79470/150‑1 (MQ=255) ccgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCg                                                                                                                                                 >  2:624425/1‑151 (MQ=255)  cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGc                                                                                                                                                <  2:217788/151‑1 (MQ=255)   gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGcc                                                                                                                                               >  2:147764/1‑151 (MQ=255)       aTGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATg                                                                                                                                           <  1:776550/151‑1 (MQ=255)         gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGcc                                                                                                                                         >  1:249819/1‑151 (MQ=255)            cTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCccgc                                                                                                                                      >  2:120939/1‑151 (MQ=255)                           ggACGGCGACCGAAAAAGGGTGAGTGATTCCCTGCGCGTACTGAAACAGGTCGCCGCGCGTACCGAAA‑CC‑GTGGTGTATCCCGACCCTTAAAACCCC‑TATCAGAATCATATGATCAA‑CCCCCTCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                                         <  1:268073/149‑1 (MQ=255)                               ggggACCGAAAAAGGGTGGGTGTTTCCCTGGGCGTCCTGGACCAGGTCGCCGCGCGTCCAGGAC‑CG‑GTGGTGTCTCTCAACCCTTTAAACCGC‑TATAAGGATCATAGGATAAA‑CACCCCCGCCGGTGCCCGCCGTTACATCGTCGAAAAc                                                                                                                    <  1:330333/147‑1 (MQ=255)                                gCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACg                                                                                                                   >  1:66045/1‑150 (MQ=255)                                  gACCGAAAAATGGTGAGTGATTCCCGGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGAC‑CG‑GTGGTGTATCTCGACCCGTTAACCCGC‑TATCAGGATCATATGATCAA‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGa                                                                                                                  <  1:220817/149‑1 (MQ=255)                                    ccGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                              >  2:292047/1‑151 (MQ=255)                                              gtgagtgaTTCCCTGCGCTTACTGGAACAGGTCGCCGCGCGTCCCGGAC‑CG‑GTGGTTTATCTCGACCCGTAAACCCGC‑TATCAGGTTCATATGATCAC‑CCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                    <  1:436089/151‑1 (MQ=255)                                              gtgagtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                    >  2:809870/1‑151 (MQ=255)                                                      tccccTGCGGGTACGGGAACAGGTCGCCGCGCGT‑CCGGAA‑CCGGTGGTTTATCTCAACCCTTAAAACCTC‑TATAAGGTTAATATGATCAA‑CCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGa                                                                                                 <  1:786507/144‑1 (MQ=255)                                                      tccccTGCGCGTACTGGAACGGTTCCCCGCCGGTACCGGAC‑CG‑GGGTTGTCTCTCAACCCTTTAACCCGC‑TATCAGATTCATATGATCAA‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTa                                                                                              <  1:361456/147‑1 (MQ=255)                                                           tGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                        >  1:675356/1‑150 (MQ=255)                                                             cgcgTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                                     >  2:353125/1‑151 (MQ=255)                                                                gTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                  >  1:496791/1‑151 (MQ=255)                                                                gTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                  >  2:342418/1‑151 (MQ=255)                                                                gTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                  >  2:352527/1‑151 (MQ=255)                                                                gTACGGGAACGGGTCGCCGGGGGTCCCGAAA‑CG‑GGGGTGTTCCTCGACCCGTAAACCCCT‑TATCAGATTTATATGACAAA‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                                   <  1:14307/150‑1 (MQ=255)                                                                          aGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGa                                                                         >  1:118343/1‑150 (MQ=255)                                                                           ggccgccgcGCG‑CCCGGAACCC‑GTGGTTTATC‑CCAACCTGTAAACCCCTTATCAGTATCATATGACCAA‑CCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                             <  2:809919/142‑1 (MQ=255)                                                                              cgccccGCTTCCCGAAC‑CC‑GGTGTGTTTCCCGACCCGTAAACCCCC‑TATCAGTATCA‑AAGAACAACCCCCCTCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAata                                                                      <  2:352243/149‑1 (MQ=255)                                                                                ccgcGCGGCCCGGAG‑CT‑GTGGTGTATCCCGAACTGTAAACCCGC‑TATCAGGATAATAAAATCAC‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGaa                                                                        <  2:354133/145‑1 (MQ=255)                                                                                      gTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                               >  2:122858/1‑148 (MQ=255)                                                                                       tACCGGAA‑CC‑GTGGTTTACCTCAACCCGTAAAACCTT‑TATCAGAAGCTAATAATCAA‑CACCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAagaaga                                                            <  1:193648/150‑1 (MQ=255)                                                                                        aCCGGGA‑CCGGTGGTGTATCCCGACCCGTTAACCCGC‑TACCAGAATAATATGATCAC‑CCCCCCCCCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGaagaag                                                             <  2:753613/149‑1 (MQ=255)                                                                                         ccGGAC‑CG‑GTGGTGTTTCTAGAACGATAAACCCGC‑TAACAGAAAAATAGAATAAA‑CCCCCCCCCGGAGCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGaagaag                                                             <  1:625527/147‑1 (MQ=255)                                                                                           cgggaatggtggtgTACCGCGAACCGTAAACCCGC‑TATCAGAATAATATGATAAA‑CCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                         <  2:769133/143‑1 (MQ=255)                                                                                            gaaccc‑GGGGTGTACCTCGACCCGTTAACCCGC‑TATCAGGATCATATGATCAA‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                        <  1:616239/146‑1 (MQ=255)                                                                                             gaaacggggttgtATCCCGAACCGTAAACCCGC‑TATCAGGAACATATGATAAC‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                         <  2:130337/139‑1 (MQ=255)                                                                                                     ggttTATCCCGAACCTTTAACCCGC‑TATAAGAATCATATGATCAC‑CCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAg                                               <  1:729306/151‑1 (MQ=255)                                                                                                     ggtgTATCTCGACCCTTAAACCCGC‑TATCAGGATCATATAATCAA‑CCCCCTCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcg                                                  <  1:815286/148‑1 (MQ=255)                                                                                                     ggtgTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                                 >  1:476491/1‑149 (MQ=255)                                                                                                        gtATCGCGAACCTTTAACCCGC‑TACCAGAACAATATAATCAA‑CCCCCCCCCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgc                                             <  1:224073/150‑1 (MQ=255)                                                                                                         tttccgaacccGTTAACCCCC‑TACCAGAATCATTTTACCAC‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATATCCTGgcg                                                  <  1:568573/135‑1 (MQ=255)                                                                                                                        aaCCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCAGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                            >  2:397193/1‑151 (MQ=255)                                                                                                                          ccGT‑TATCAGAATCATATGATCAA‑CCCCCTCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGa                           <  1:767531/150‑1 (MQ=255)                                                                                                                                   atgctCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg                  >  2:255568/5‑151 (MQ=255)                                                                                                                                    ggttCATATGACAAA‑CCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc                    <  2:578221/145‑1 (MQ=255)                                                                                                                                    ggATCAAAGGAACAA‑CCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc                    <  2:779562/148‑1 (MQ=255)                                                                                                                                    gaaTCATATGATAAC‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                   <  1:510719/147‑1 (MQ=255)                                                                                                                                            tGAACAA‑CCCCCTCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgt            <  1:335536/148‑1 (MQ=255)                                                                                                                                              aTCAA‑CCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCat        <  1:585954/150‑1 (MQ=255)                                                                                                                                              aTCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCat        >  2:351142/1‑150 (MQ=255)                                                                                                                                                    cacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCg  >  1:257444/1‑151 (MQ=255)                                                                                                                                                     |                                                                                                                                                      CCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAA‑CC‑GTGGTGTATCTCGAACCGTTAAACCGC‑TATCAGGATCATATGATCAA‑CACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCG  >  NC_000913/1376361‑1376654

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: ‑