Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	42.2%	69.5 / 14.5	45	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (21/5);  new base C (0/19);  total (21/24)
Fisher's exact test for biased strand distribution p-value = 3.06e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCGG  >  NC_000913/1376360‑1376655                                                                                                                                                    |                                                                                                                                                       aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                                   <  2:713924/151‑1 (MQ=255)    gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGcc                                                                                                                                                >  1:200123/1‑151 (MQ=255)      cgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGa                                                                                                                                              <  1:20419/151‑1 (MQ=255)          gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                                          <  2:116889/151‑1 (MQ=255)            ccTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccg                                                                                                                                        <  2:499997/151‑1 (MQ=255)                gccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGt                                                                                                                                    >  2:668384/1‑151 (MQ=255)                         cggggAGGGCGACCGCAAAAGGGTGAGTGATCCCCTGCGCTTCGGGGAACGGGTCGCCGCGCGTACAGACACC‑GGGGTGTTTCTCGACCCGTAAAC‑CCTCTATCTGTACCATGTGATCACCCCCCCCGCCGATGCCCGCCGTTACAtc                                                                                                                              <  1:738259/145‑1 (MQ=255)                                   gACCGCAAAATGGAGAGTGATTCCCTGCGCGTACTGGAACAGGCCGCCGCGCGTACCGGCACC‑GTGGTGTATCCCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCACGCCGTTACATCGTCGACAACGATc                                                                                                                 >  1:877468/1‑151 (MQ=255)                                     ccGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                               >  2:127764/1‑151 (MQ=255)                                         aaaaGGGTGAGTGATCCCCGGCGCGTCCCGGAACGGGCCGCCGCGCGTCCCGGACCG‑GTGGTGTATCCCGACCCGTAAAC‑CCGCTATAAGAATCATATGATAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGa                                                                                                                   <  2:588649/143‑1 (MQ=255)                                             tGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGt                                                                                                       >  1:478215/1‑151 (MQ=255)                                                   gtgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                                     >  2:670611/1‑147 (MQ=255)                                                   gtatttCCCGGCGTGTACTGGAACGGGTCGCCGCGCGTCCCGGACCG‑GTGGTGTATCTCGACCCTTTAAA‑CCGCTATCAGAATCATATGATAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAg                                                                                                   <  2:699500/145‑1 (MQ=255)                                                    tgaTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAtt                                                                                                >  2:793652/1‑151 (MQ=255)                                                         cctggccgttatgggAACGGGCCGCCGCGGGTACGGGATCG‑GGGGTTTACCTGGACCCATAAAC‑CCCTTATGAGAATCAAATATTCAACCCCTTCTCGGGTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATc                                                                                             <  2:675021/136‑1 (MQ=255)                                                           cTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                         >  1:522093/1‑151 (MQ=255)                                                             gcgcGTACGGAAACGGGTCGCCGCGCGTCCCGGACCC‑GTGGTGTATCTCGAACCTTAAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                         <  2:739000/149‑1 (MQ=255)                                                              cgcgTCCTGAAACGGGTCGCCGCGCGTCCCGGACCC‑GTGGTGTATCCCGACCCTTTAAC‑CCGCTATCAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAt                                                                                       <  2:666151/150‑1 (MQ=255)                                                                cgTCCTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAC‑CCGCTACCAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                                     <  2:82477/150‑1 (MQ=255)                                                                 gTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                   >  2:452468/1‑151 (MQ=255)                                                                  tACTGAAACGGGCCGCCGCGCTTCCCGGACCG‑GGGGTGTATCGCGACCCGTTAAC‑CCGTTAACGGGAACATATAACCACCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                   <  1:185511/150‑1 (MQ=255)                                                                     tGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                                >  2:797696/1‑150 (MQ=255)                                                                     gggAACGGGTCGCCGCGCGTCCCGGACCC‑GTGGTTTATCCCGACCCGTTAAC‑CCGCTATCAGGATAATATGATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTAt                                                                                 <  2:71980/148‑1 (MQ=255)                                                                        agcgggcccccgcGCTTA‑CGGAACCGGGGGTGTATCTCAACCCGTAAAC‑CCGATACCAGGATTATATGATCACCCCCCTCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACAt                                                                            <  1:643647/142‑1 (MQ=255)                                                                            ggccgccgcGCGT‑CCGGAACCGGTGGTTTATCCCGACCCTTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                                        <  1:767709/148‑1 (MQ=255)                                                                              tCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAatat                                                                      >  2:127335/1‑151 (MQ=255)                                                                                     gcgTCCCGGACCG‑GTGGTGTTTCTCGACCCTTTAAC‑CCGCTAACAGGATCATATGATCAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaag                                                                 <  2:200158/149‑1 (MQ=255)                                                                                          ccGGACCG‑GGGGTGTATCTCAAACCTTAAAC‑CCGCTATAAGGATCATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                          <  1:668297/151‑1 (MQ=255)                                                                                            ggAACC‑GTGTTTTATCTCGAACCTTAAAC‑CCACTATCAGAATCATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                          <  1:851997/149‑1 (MQ=255)                                                                                            ggAACC‑GTGGTTTATCCCGACCCTTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                        <  2:609921/151‑1 (MQ=255)                                                                                              aaCG‑GTGGTGTATCTCGAACCTTAAAC‑CCGCTATCAGAATCATAGAAACAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                        <  2:545446/149‑1 (MQ=255)                                                                                               accgggggtgTACCCCAAACCGTAAAC‑CCGCTACCAGGATAATAAGAACAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATaa                                                          <  1:785152/141‑1 (MQ=255)                                                                                                cc‑GTGGTGTATCTCAAACCTTAAAC‑CCGCTATCGGGATCATATGACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                         <  1:26163/146‑1 (MQ=255)                                                                                                cc‑GTGGTGTATCTCAAACCTTAAAC‑CCCCTATCAGTATCATATAATCACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgc                                                    <  2:306864/151‑1 (MQ=255)                                                                                                     ggtgTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgcgc                                                  >  2:649314/1‑149 (MQ=255)                                                                                                      gtgtATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAgg                                               >  2:759328/1‑151 (MQ=255)                                                                                                               gAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                                      >  2:492251/1‑151 (MQ=255)                                                                                                                   cGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACa                                   >  2:330630/1‑150 (MQ=255)                                                                                                                    cttAAACCCGCTATCAGAATCAAATAACAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCAt                                       <  1:297624/145‑1 (MQ=255)                                                                                                                        aa‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                             >  2:438252/1‑151 (MQ=255)                                                                                                                                aTCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCt                      >  2:135382/1‑151 (MQ=255)                                                                                                                                   aGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg                   >  1:550514/1‑151 (MQ=255)                                                                                                                                    ggATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGt                  >  2:60983/1‑151 (MQ=255)                                                                                                                                        cATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg              >  1:313142/1‑151 (MQ=255)                                                                                                                                            tGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGc           >  2:352573/1‑150 (MQ=255)                                                                                                                                                    acCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCgg  >  1:249604/1‑151 (MQ=255)                                                                                                                                                    |                                                                                                                                                       ACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCGG  >  NC_000913/1376360‑1376655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑