Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	41.5%	53.3 / 14.9	41	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (20/4);  new base C (0/17);  total (20/21)
Fisher's exact test for biased strand distribution p-value = 4.70e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376358‑1376652                                                                                                                                                         |                                                                                                                                                    ttACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACAccc                                                                                                                                                  >  1:515013/1‑151 (MQ=255)     cgccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGc                                                                                                                                              <  2:508096/151‑1 (MQ=255)      gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTc                                                                                                                                                <  1:299111/148‑1 (MQ=255)         gATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGAt                                                                                                                                          >  1:814423/1‑151 (MQ=255)          aTGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATg                                                                                                                                         <  2:743874/151‑1 (MQ=255)                tCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCccgcc                                                                                                                                   >  2:519615/1‑151 (MQ=255)                              ggACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGa                                                                                                                      >  1:725715/1‑150 (MQ=255)                                    cgacaaaaaatTGGTGATTGTTCCCCTGGTCTTCCGGTAACGGCTCGCCGCGCTGCCCGAAACG‑TT‑GTTTTACCACGAACTGTAAAA‑CCGCTATCG‑GGATA‑ATATAATCACCCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                               <  1:226143/144‑1 (MQ=255)                                     gACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATc                                                                                                              >  1:647681/1‑151 (MQ=255)                                       ccGCAAAGGGGTGAGTTTTTCCCTCCGCGTGCGGAACCGGGCCGCCGCGCGTCCCGG‑ACC‑GTGGGTTTACCCCAAACCTTAAAC‑CCGTTTTCA‑GGAAA‑AGATAATCAACCCCCGCGCCAATCCCCGCCGTTACATCGTCGAAAACGAt                                                                                                               <  1:626841/148‑1 (MQ=255)                                        cGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                            >  1:589791/1‑150 (MQ=255)                                                        aTTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTa                                                                                            >  1:442280/1‑150 (MQ=255)                                                            ccggcggttccTGGAACAGGTCGCCGCGGGTACCGGAACC‑GG‑GGTGTATCTCGACCCTTTAAC‑CCGATATAA‑GGATA‑ATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGc                                                                                       <  2:424344/141‑1 (MQ=255)                                                               gggcgTACTGAAAAGGGCCGCCGCGCGTACCGGACCC‑GT‑GTTGTACCTCGAACCGTAAAC‑CCGCTATCA‑GGATA‑ATATAACCAACCCCCTCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAt                                                                                    <  2:423063/149‑1 (MQ=255)                                                               gcgcGTAGTGGACGAGGCCGCCGCGCGTCCCGGACCC‑TT‑GTTGTATC‑CCAACCCTTAAACCCGCTATAA‑GTATC‑ATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCg                                                                                      <  1:568024/149‑1 (MQ=255)                                                                 gcgTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAttt                                                                                  >  2:903611/1‑151 (MQ=255)                                                                    tACTGAAACAGGTCGCCGCGCGTCCCGGACCC‑GT‑GGTTTATCTCGACCCTTAAAC‑CCGCTAACA‑GGATC‑ATATGACCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                                 <  2:694118/149‑1 (MQ=255)                                                                     cgtGGAACAGTTGGCCGCGCGTACCGAACCC‑GG‑GGTGTGTCCCGCAGCTTTAAC‑CTTAAATCA‑‑GATCAAAATGACCCCCACCCTCCCTGTGTCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGAtt                                                                                   <  1:587295/144‑1 (MQ=255)                                                                       tGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                             >  1:281574/1‑150 (MQ=255)                                                                       tGGAACAGGCCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                             >  2:477913/1‑150 (MQ=255)                                                                          accAGGCCCCCGCGCGTACCGGACCC‑GT‑GGTTTCTCCCGAACCGTAAAC‑CCGCTACCA‑GGAAA‑ATAAAACCACCCCCCCCCCTGAGCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCt                                                                                <  1:503984/142‑1 (MQ=255)                                                                          aacgggcccccgcGCGTCCGGGACCG‑GT‑GTTTTATC‑CCAACCCTTAAACCCGCTACCA‑GGATA‑ATATAACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                           <  1:959164/140‑1 (MQ=255)                                                                              ggTCGCGGCGCGTACCGGAACG‑GT‑GGTTTCTCTCAACCCTTTAAC‑CCGCTATCA‑GGATC‑ATATGATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGa                                                                       <  2:174476/149‑1 (MQ=255)                                                                                    ccggcgTACCCGAACCGGT‑GTTGTCTCCCGAACCGTAAAC‑CCGATAGCA‑GAATA‑ATATGAACAACCCCCCCGCCGATCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAat                                                                     <  1:184706/143‑1 (MQ=255)                                                                                       gcgTCCGGGAGCC‑GT‑GGTGTCTCTCAAACCGTAAAC‑CCGCTATCA‑GAATA‑ATATAAACACCCCCCTCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                             <  1:636802/150‑1 (MQ=255)                                                                                         gTACCGGACCG‑GT‑GGTGTATCTCGACCGGTTAAC‑CCTCTATCA‑GGATA‑ATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAagaaga                                                          <  2:132982/151‑1 (MQ=255)                                                                                                        ggttTACCTCGACCCGTTAAC‑CCGCTATCA‑GGATA‑ATAGAACCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCa                                              <  2:29661/150‑1 (MQ=255)                                                                                                        ggtgTATCTC‑AACCTGTAAA‑ACGCT‑TCACGGAACAATATGAACACCCCCCCCGCCCTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                   <  1:95431/145‑1 (MQ=255)                                                                                                           tgtacctgAACCCTTAAACCCGTTACAA‑GAATA‑ATATAAAAAACCCCCTCGCAGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGgc                                                 <  1:234162/138‑1 (MQ=255)                                                                                                               ctcGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGc                                      >  2:585417/1‑151 (MQ=255)                                                                                                                tcGGACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGCTCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATACCGAAGAAGATAACCTGGCGCAGGCGCt                                        >  1:398482/1‑148 (MQ=255)                                                                                                                   aaCCTTTAAC‑CCGATATCA‑GAATA‑ATATAAACACCCCCCTCCCGGAGCCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                                   <  1:634999/150‑1 (MQ=255)                                                                                                                   aaCCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATg                                   >  2:283611/1‑150 (MQ=255)                                                                                                                       gTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAAc                              >  2:193449/1‑151 (MQ=255)                                                                                                                        ttAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATATCCTGGCGCAGGCGCTGCATGACAAcc                             >  2:537879/1‑151 (MQ=255)                                                                                                                                     cA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                 >  2:450933/1‑151 (MQ=255)                                                                                                                                          aTC‑ATATGACCACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCa             <  2:716456/151‑1 (MQ=255)                                                                                                                                               tatGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgt          >  1:184160/1‑150 (MQ=255)                                                                                                                                                  gATCAACACCCTCGCCGATGCCCGCAGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTAGGTCATGTGCa       >  1:695980/1‑150 (MQ=255)                                                                                                                                                      aaCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCTCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATAtt   >  2:296412/1‑150 (MQ=255)                                                                                                                                                      aaCACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTg  >  1:369243/1‑151 (MQ=255)                                                                                                                                                        cacCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                 <  2:151229/134‑1 (MQ=255)                                                                                                                                                         |                                                                                                                                                    TTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GT‑GGTGTATCTCGAACCGTTAAA‑CCGCTATCA‑GGATC‑ATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTG  >  NC_000913/1376358‑1376652

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑