Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	47.5%	49.3 / 11.9	40	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (18/3);  new base C (0/19);  total (18/22)
Fisher's exact test for biased strand distribution p-value = 1.19e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCGG  >  NC_000913/1376357‑1376655                                                                                                                                                         |                                                                                                                                                       cTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGG‑CGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACAcc                                                                                                                                                      >  1:1201668/1‑151 (MQ=255)      cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGc                                                                                                                                                 >  2:443475/1‑151 (MQ=255)       gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGcc                                                                                                                                                >  1:2161786/1‑151 (MQ=255)       gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGG‑TGAGTGATGCCCGGCGCGTACTTGATTAGTTTGCCGCGCCGACCGCCACC‑GGGGTGTAT‑CTCGAACCGTTAAC‑CCCCTACCAGGCCCATATCATCACCAccc                                                                                                                                                     <  1:4041383/146‑1 (MQ=255)        ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                               <  1:352151/151‑1 (MQ=255)                  cgccgcGTAGCCTGGACGGCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccgcc                                                                                                                                      <  2:917541/150‑1 (MQ=255)                               ggACGGCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCTTCCCGGACCC‑GTGGTTTAT‑CTCGACCCGTAAAC‑CCGCTATCAGGTTCATATAACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGaa                                                                                                                        <  2:4076030/151‑1 (MQ=255)                                    gCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACg                                                                                                                    >  2:116010/1‑150 (MQ=255)                                        ccGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGACCC‑GTGGTGTAT‑CTCGACCCTTTAAC‑CCGCTATAAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                                  <  2:3700105/148‑1 (MQ=255)                                             aaaTGGTTGAGGGCTTCCCTGCGGTTACTGGAACAGGTCGCCGCGGTTACCGAACCC‑GTGGTGTAT‑CTCAACCCTTTAAC‑CCCCTTTCAGTATCATTTAATAAACCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTa                                                                                                              <  2:3226173/148‑1 (MQ=255)                                                        tgttccccggggcgTACTGAAACGGGTCGCCGCGCGT‑CCGGAACCGGTGTTTTAT‑CTC‑AACCCTTAAACCCGTTATCAGGATCATATAATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                                 <  2:2704522/139‑1 (MQ=255)                                                             cccGGCGCTTACTGAAACGGGTCGCCGCGCGTACCGGACCC‑GGGGTTTAT‑CCCGACCCTTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                                 <  1:3940229/145‑1 (MQ=255)                                                                 gcgcGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAt                                                                                       >  2:1398812/1‑151 (MQ=255)                                                                   ggttACTGAAAAAGTTCGCCGCGCGTCCGGGACCC‑GTGGTGTAT‑CTC‑AACCCTTAAACCCGCTATCAGGATAATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                                     <  2:623356/148‑1 (MQ=255)                                                                      tACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                   >  2:1076248/1‑150 (MQ=255)                                                                         tGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                                >  2:3656460/1‑150 (MQ=255)                                                                         tGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                                >  2:3689286/1‑150 (MQ=255)                                                                         tGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                                >  2:1114058/1‑150 (MQ=255)                                                                                     ccgcGCGTCCCGGACCC‑GTGGTGTAT‑CTCAAACCTTTAAC‑CCGCTATAAGGATCATATGATCAACCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAatat                                                                      <  2:2267561/148‑1 (MQ=255)                                                                                         gcgTACCGGACCG‑GGGGTGTAT‑CTCGACCCGTTAAC‑CCGCTATCAGGATCATATGATAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaa                                                                  <  2:590195/148‑1 (MQ=255)                                                                                         gcgTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                                >  1:3032619/1‑150 (MQ=255)                                                                                         gcgGACGGGAACC‑GTGTTGTAT‑CTCGACCCGTTAAC‑CCGTTATCAGGATCATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaag                                                                 <  1:928756/149‑1 (MQ=255)                                                                                            tACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                                >  2:1903358/1‑147 (MQ=255)                                                                                            gaaccgAACC‑GGGGTTTAACCTCGAACCGTAAAC‑CCTCTACAAGAATAAAATAACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAagaaga                                                             <  1:2960353/146‑1 (MQ=255)                                                                                                ggAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                        >  1:671723/1‑151 (MQ=255)                                                                                                 gAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCt                                                       >  2:794268/1‑151 (MQ=255)                                                                                                   accgggggttTAT‑CTCGACCCTTTAAC‑CCGCTATCAGGATAATATGATCAACCCCCGCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                         <  1:2924166/142‑1 (MQ=255)                                                                                                       gtggtgTCT‑CTCGACCCTTTAAA‑CCGTTATAAGAATAATATAATCAACCCCCCCCCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCt                                                       <  1:4001886/146‑1 (MQ=255)                                                                                                           tttAT‑CTCAACCTGTAAAC‑CCGCTATCAGGATCATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                     <  1:3939521/142‑1 (MQ=255)                                                                                                           tgtAC‑CTCGACCCTTAAAC‑CCTCTATCAGGACCATATGATCACCCCCCCCCCCGATTCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCa                                                 <  1:289501/148‑1 (MQ=255)                                                                                                                 gtcgagcagaaaga‑CCGCTATGGGGATAATATGATCCCCACCCTCGCCGATGCCCGGCGTTACATCGTCGAAAAAAAAATTAAACATGAACAGATTATAGGCGATTTATATCACCTGAATATCGAAGAAGATAACCTGGAGCAGGCGCTGc                                         >  1:2498988/14‑151 (MQ=255)                                                                                                                            aaacccgaattCATGATCATATTAAAAACCCCCTCGCCAATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATACCCTGGCGCAGgcgc                                            <  2:2670928/128‑1 (MQ=255)                                                                                                                            aaacccGCAACCAGGATCATATGACAACCCCCCCCGCGGAGCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCa                                        <  1:3954013/138‑1 (MQ=255)                                                                                                                                 cGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc                          >  2:3119315/1‑151 (MQ=255)                                                                                                                                 cGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAcc                          >  2:2734954/1‑151 (MQ=255)                                                                                                                                   cTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTg                        >  1:1408594/1‑151 (MQ=255)                                                                                                                                         ggttCATATGATCAACCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGt                  <  2:913031/148‑1 (MQ=255)                                                                                                                                              atatGACCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTc                 <  2:391885/147‑1 (MQ=255)                                                                                                                                                 tgctCAACCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtg              <  2:1500452/144‑1 (MQ=255)                                                                                                                                                      aaCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTg     >  1:3667242/1‑151 (MQ=255)                                                                                                                                                         acCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCgg  >  2:4099459/1‑151 (MQ=255)                                                                                                                                                         |                                                                                                                                                       CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGG‑TGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTAT‑CTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGCGG  >  NC_000913/1376357‑1376655

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑