Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,376,505	0	A	C	50.0%	49.3 / 13.6	42	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (20/1);  new base C (0/21);  total (20/22)
Fisher's exact test for biased strand distribution p-value = 8.17e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAAT‑GGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGC  >  NC_000913/1376357‑1376653                                                                                                                                                        |                                                                                                                                                     cTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAAT‑GGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACAcc                                                                                                                                                    >  2:579307/1‑151 (MQ=255)       gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAAT‑GGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGcc                                                                                                                                              >  1:656681/1‑151 (MQ=255)             gACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAAT‑GGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGcc                                                                                                                                        >  1:294472/1‑151 (MQ=255)                               ggccGGCGCCCGAAAAAG‑GGTGAGTGATTCCCTGCGCGTACGGAAACAGGTCGCCGCGCGCCCCGGACCC‑GTGGTGTATCTCGACCCGTTAAC‑CCGCTATCAGGATCATATGAACACCCCCCTCGCCGATGCCCGCCGTTACAtcgtc                                                                                                                         <  2:269196/145‑1 (MQ=255)                               ggACGGCGCCCGAAAAAG‑GGGGAGTGATTCCCTGCGCTTACGGAAACAGGTCGCCGCGCGTCCCGGACCC‑GTGGTGTATCCCGACCCTTTAAC‑CCGCTATCAGAATAATATGATCAACCCCCCCGCCGTTGCCCGCCGTTACATCGTCGaa                                                                                                                      <  1:110978/151‑1 (MQ=255)                                   ggCGACCAAAAAAG‑GGTGGGTGTTCCCCTGCGCGTACAGGAAGGGGTCCCCGCGCTTACCGAACCC‑GGGTTTTATCTCGAACCTTAAAA‑CCGTTATAGGGATAATATGACAAACCCCCCCGCGGATGCCCGCCGTTACATCGTCGAAAACg                                                                                                                  <  2:494513/151‑1 (MQ=255)                                        ccGCAAAAT‑GGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                             >  2:110506/1‑151 (MQ=255)                                         ccaaaaaTGGGTGAGTGATTCCCGGCGCGTACTGGAACAGGTCGCCGCGCGTCCCGGAACC‑GTGGTGTATCTCGACCCTTAAAC‑CCGCTATCAGGATCATATGATAAACCCCCTCGCCTATGCCCGCCGTTACATCGTCGaaa                                                                                                                     <  2:268533/140‑1 (MQ=255)                                            aaaaT‑GGTGAGTGATTCCCTGCGGGTCCGGGAACAGGTCGCCGCGCGTCCGGGACCC‑GGGGTGTATCTCGACCCGTTAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCtt                                                                                                             <  1:69522/147‑1 (MQ=255)                                            aaaaT‑GGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAAc                                                                                                         >  2:699949/1‑151 (MQ=255)                                               attggtgtgggttccccTGCGCATCCGGGAACGGGTCCCCGCGTATACCGGACCG‑GTGTTGTTGCGCAACCCGTTACC‑CTCTTATGAGGATTATATTTTCAACACCCTAGCGATTGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                           <  2:548888/133‑1 (MQ=255)                                                  ggTGAGTTATCCCCGGCGCGTACGGGAACGGGTCGCCGCGCGCCCCGAACCC‑GTGGTGTATC‑CCAACCCTTAAACCCGCTACCAGGATAATATGACCACCCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGt                                                                                                     <  2:587951/150‑1 (MQ=255)                                                     gagtgtTTCCCTGGGCGTACTGAAACAGGTCGCCGCGCGTACCGGAACG‑GTGGTGTATCGCGAACCTTAAAC‑CCGCTATCAGGATAATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACa                                                                                                  <  2:294424/150‑1 (MQ=255)                                                        tgaTCCCCTGCGCTTACTGGAACAGTTCCCCGCGC‑TACCGGGACCGGTGTTGTTTCTCAACCCTTAAAA‑CCGCTACCAGGATCATATGATCACCCCCCTCGCCTATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGAt                                                                                               <  1:396101/150‑1 (MQ=255)                                                                          ggAGCAGGTCGCCGCGCGT‑CCGGAACCGGTGGTTTATC‑CCAACCCTTAAACCCGCTACAAGGATAATATGATCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATc                                                                              <  2:473174/149‑1 (MQ=255)                                                                                 gTCGCCGCGCGTCCCGGACCG‑GTGGGGTATCTCGAACCGTAAAC‑CCGCTATCAGGATCATATGAAAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGaa                                                                       <  1:491689/149‑1 (MQ=255)                                                                                  tCGCGGCGCGTACGGGACCG‑TTGTTTTTTCTCAAACCTTAAAA‑CCGTTACCGGGATCATATAATCACCCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAata                                                                     <  1:641284/150‑1 (MQ=255)                                                                                   cgccgcGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATc                                                                   >  1:604500/1‑151 (MQ=255)                                                                                     ccgcGCGTCCGGGACCC‑GTGGTGTATCGCGACCCGTAAAC‑CCGCTATCAGGATAATAGGACCACCCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                                  <  2:368728/150‑1 (MQ=255)                                                                                     ccgcGCGTCCCGGACCC‑GTGTTTTTTC‑CCAACCCTTAAACCCGTTATCAGGATAATATGACAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                                 <  1:673977/151‑1 (MQ=255)                                                                                     ccgcGCGTACCGGAACG‑GGGGTGTATCTCGAACCTTTAAA‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                                 <  1:306169/151‑1 (MQ=255)                                                                                      cgcgcgTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                                 >  1:403359/1‑150 (MQ=255)                                                                                       gcgcgTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                                 >  1:222628/1‑149 (MQ=255)                                                                                          cgTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCgaaga                                                              >  1:236701/1‑149 (MQ=255)                                                                                           gtcccGGACCC‑GTGGTGTATCTCGAACCGTTAAC‑CCGCTATCAGAATAATATAATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGaagaag                                                            <  1:496179/147‑1 (MQ=255)                                                                                             aCCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                          >  1:34152/1‑150 (MQ=255)                                                                                               cGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAc                                                       >  1:552551/1‑151 (MQ=255)                                                                                                  accc‑GTGGTGTATCTCAACCCTTTAAC‑CCGTTATCAGGATAATATGATAAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                    <  1:682625/149‑1 (MQ=255)                                                                                                   aCC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTgg                                                   >  2:230694/1‑151 (MQ=255)                                                                                                         gttgtACCTCGAACCGTTAAC‑CCGTTATCAGGATAATATATTCACCCCCCTCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                                    <  2:644786/143‑1 (MQ=255)                                                                                                         ggtgTTTCTCAACCCTATAAC‑CCTCTATCAGGATCATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCa                                               <  2:334460/150‑1 (MQ=255)                                                                                                              aTCTCAACCCGTAAAA‑CCGCTATAAGGTTAATATGATAACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAgg                                             <  1:355692/147‑1 (MQ=255)                                                                                                                             acccGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACcgcg                           <  1:32390/149‑1 (MQ=255)                                                                                                                               ccGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGAc                         >  1:227095/1‑151 (MQ=255)                                                                                                                                      cAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTc                   >  2:494448/1‑150 (MQ=255)                                                                                                                                      cAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                  >  1:520996/1‑151 (MQ=255)                                                                                                                                      cAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCg                  >  2:622871/1‑151 (MQ=255)                                                                                                                                       aGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCgg                 >  1:291694/1‑151 (MQ=255)                                                                                                                                              tatGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgtg          >  2:141260/1‑151 (MQ=255)                                                                                                                                                tGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGc         >  2:427535/1‑150 (MQ=255)                                                                                                                                                  aTCACCACCTTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACCTGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCa        >  2:382020/1‑149 (MQ=255)                                                                                                                                                     aaCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCatat     <  1:552731/149‑1 (MQ=255)                                                                                                                                                      acacCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGc  >  2:554210/1‑151 (MQ=255)                                                                                                                                                        |                                                                                                                                                     CTTACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAAT‑GGTGAGTGATTCCCTGCGCGTACTGGAACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCATATTGC  >  NC_000913/1376357‑1376653

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: ‑