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%	51.3 / 16.9	42	T158P (ACC→CCC)	ycjR	putative TIM alpha/beta barrel enzyme
Reads supporting (aligned to +/- strand):  ref base A (17/4);  new base C (0/21);  total (17/25)
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

ACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCAT  >  NC_000913/1376360‑1376648                                                                                                                                                     |                                                                                                                                                aCCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTc                                                                                                                                            >  2:663662/1‑151 (MQ=255)    gccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGcc                                                                                                                                         <  2:992797/151‑1 (MQ=255)     ccgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCg                                                                                                                                        <  1:500058/151‑1 (MQ=255)      cgATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCg                                                                                                                                        >  2:99027/1‑150 (MQ=255)       gATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGAt                                                                                                                                      >  2:242490/1‑151 (MQ=255)            ccTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGccc                                                                                                                                  <  1:946450/150‑1 (MQ=255)             cTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccgc                                                                                                                                >  2:930606/1‑151 (MQ=255)               cgccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCccgcc                                                                                                                               <  2:317139/150‑1 (MQ=255)                gccgcGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGt                                                                                                                             >  1:780545/1‑151 (MQ=255)                    cgTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTAc                                                                                                                          >  2:657066/1‑150 (MQ=255)                           tGGGCGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACAtcgtcg                                                                                                                   >  1:887077/1‑150 (MQ=255)                                ggggacccaaaagTGGGGGGTGTTCCCCTGCGCGTCCGGA‑AACAGCCCGCCGCGCGTCCCGGACCG‑GGGGTGTATCTCGACCCGTAAAC‑CCGCTTTAAGGATCATATGAACACCCCCCCCGCCGAGGCCCGCCGTTACATCGTCGaaaa                                                                                                               <  1:735054/140‑1 (MQ=255)                                ggCCACCGCAAAAGGGGGAGTAATCCCCTG‑GGGTTTTGGAAAGGGGGCGCCGCGC‑TTCCGGAACCGGTGGTGTATCCCG‑ACCTTTAAACCCGCTATCGGTTTCATATGATCAACCCCCCCGCCGAGGCCCGCCGTTACATCGTCGaaaa                                                                                                               <  2:697087/149‑1 (MQ=255)                                  cGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGAt                                                                                                           >  1:225346/1‑151 (MQ=255)                                         aaaaGGGTGGGTTATCCCCTGCGCGTCCGGG‑AACGGGCCGCCGCGCTTGCCGGACCC‑GTGGTGTATCTCAACCCTTTAAC‑CCCCTATCAGGCTCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTaa                                                                                                      <  1:602941/149‑1 (MQ=255)                                           aagggTGAGTTATTCCCTGCGCGTACGGG‑AACAGGTCGCCGCGCGTACCGAACCG‑GTGGTGTATCCCAAACCGTAAAC‑CCGCTATCAGGTTCATATAAACAACCCCCACGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACAt                                                                                                  <  1:53063/148‑1 (MQ=255)                                             tGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGt                                                                                                >  2:806828/1‑151 (MQ=255)                                                 gagtgaTTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GCGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTACACATGTAc                                                                                              >  1:571249/1‑149 (MQ=255)                                                    tgaTTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGCCGAAAACGATCTTAAACATGTACAGAtt                                                                                         >  2:523881/1‑151 (MQ=255)                                                       tccccTGCGCGTACTGG‑AACGGGTCGCCGCGCGTACCGGACCC‑GTGGTGTATCTCGACCCTTTAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTAc                                                                                              <  2:754218/141‑1 (MQ=255)                                                         cccTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCgg                                                                                    >  1:835905/1‑151 (MQ=255)                                                         cccGGCGCGTCCGGA‑AACGGGCCGCCGCGGTTCCCGGACCC‑GTGGTTTATCTCGACCCGTAAAC‑CCGCTATCAGGATAATATGATCACCCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCgg                                                                                    <  2:989552/151‑1 (MQ=255)                                                                 gTACGGG‑AACAGGTCGCCGCGCGTACCGGAACG‑GTGGTGTATCTCGAACCGTAAAC‑CCGCTATAAGGATCATATGATAAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                             <  2:691071/150‑1 (MQ=255)                                                                      gg‑AACGGGTCGCCGCTCGTCCCGGACCG‑GTGGTGTATCGCGACCCGTTAAC‑CCGCTATAGGGATTATATAACAAACCCCCTGTCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                       <  1:243308/151‑1 (MQ=255)                                                                      gg‑AACAGGTCGCCGCGCGTCCCGAACCT‑GGGGTGTATCTCAACCCGTAAAC‑CCGCTATCAGGATCATTTGATAACCCCCCCCGCCGTTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcac                                                                       <  2:992226/151‑1 (MQ=255)                                                                         aacgggcgcccgcGCGCCCCGAACCG‑GGGGTGTACCGCGACCCTTAAAC‑CCGCTAACAGGATCATAAGACAAACCCCCTCCCCGACGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTc                                                                             <  1:558530/134‑1 (MQ=255)                                                                          aCAGGTCGCCGCGCGTACCGGAACG‑GTGGTTTATCCCAACCCGTTAAC‑CCGCTATAAGGATCATATAACCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATcaca                                                                      <  2:40720/149‑1 (MQ=255)                                                                                 gccgcGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                             >  1:21708/1‑151 (MQ=255)                                                                                  ccgcGCGTCCGGGACCG‑GTGGTTTCTCTCAAACCTTAAAC‑CCGCTATCAGGATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCga                                                            <  2:132479/151‑1 (MQ=255)                                                                                  ccgcGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                             >  2:371942/1‑150 (MQ=255)                                                                                  ccgcGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCg                                                             >  1:719553/1‑150 (MQ=255)                                                                                            cGGACCG‑GTGGTGTACCTCAACCCGTAAAC‑CCGCTATCAGGATCATATGATCACCCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGaagaag                                                       <  1:672950/146‑1 (MQ=255)                                                                                             ggACCC‑GTGGTGTATCTCAACCCGTAAAA‑CCGCTATCAGAATAATATGACCAACCCCCCCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGAt                                                     <  2:663586/147‑1 (MQ=255)                                                                                                 actgtgttctacctcGACCCTTTACC‑CCGCTATAGGGATAATAAAACAAACCCCCCCCCCGACGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATACCCTg                                               <  1:29105/138‑1 (MQ=255)                                                                                                  cctgggtgTTTCACGACCGTTTAAC‑CCGCTTGAAGAATAATAAGACCACCCCCCCCGCCTATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAAcc                                                 <  1:631071/143‑1 (MQ=255)                                                                                                         gtATCTCGACCCTTAAAC‑CCGCTATCAGAATCATATGATCAACCCCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGgc                                       <  2:639425/150‑1 (MQ=255)                                                                                                             ctaaacccGTTAAC‑CCGTTTTAGGGATAATATGACAAACCCCCTCGCGGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTg                                               <  2:199775/132‑1 (MQ=255)                                                                                                               cGAGCCATTAAA‑CCGCTACCAGAATAAATTGACCATCCCCCTCCCCAGTGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGc                                  <  2:650426/149‑1 (MQ=255)                                                                                                                  aCCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGAc                             >  2:984078/1‑151 (MQ=255)                                                                                                                                            atGACCAACCCCCCCCCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCAtgtg     <  1:527163/150‑1 (MQ=255)                                                                                                                                               aTCACCACCCTCGCCTATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCat  <  2:270771/150‑1 (MQ=255)                                                                                                                                               aTCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCat  >  1:663614/1‑150 (MQ=255)                                                                                                                                                     |                                                                                                                                                ACCGCCGATGACCTCGCCGCGTAGCCTGGACGGCGACCGCAAAATGGTGAGTGATTCCCTGCGCGTACTGG‑AACAGGTCGCCGCGCGTACCGGAACC‑GTGGTGTATCTCGAACCGTTAAA‑CCGCTATCAGGATCATATGATCAACACCCTCGCCGATGCCCGCCGTTACATCGTCGAAAACGATCTTAAACATGTACAGATTATCGGCGATTTCTATCACATGAATATCGAAGAAGATAACCTGGCGCAGGCGCTGCATGACAACCGCGACCTGCTCGGTCATGTGCAT  >  NC_000913/1376360‑1376648

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: ‑