Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,510,395	0	C	A	42.9%	87.9 / 23.5	49	S131R (AGC→AGA)	ydcR	putative DNA‑binding transcriptional regulator and putative aminotransferase
Reads supporting (aligned to +/- strand):  ref base C (25/3);  new base A (0/21);  total (25/24)
Fisher's exact test for biased strand distribution p-value = 5.18e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACTCGAGATGAAGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTGCCGGGGCGTTAGAGGCATT  >  NC_000913/1510246‑1510541                                                                                                                                                           |                                                                                                                                                   aCTCGAGATGAAGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGc                                                                                                                                                    >  2:579186/1‑150 (MQ=255)   tCGAGATGAAGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCaa                                                                                                                                                  >  1:142821/1‑150 (MQ=255)   tCGAGATGAAGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCaa                                                                                                                                                  >  2:709398/1‑150 (MQ=255)    cGAGATGAAGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCaaa                                                                                                                                                 >  2:118078/1‑150 (MQ=255)          gAAGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGcc                                                                                                                                           <  1:409338/150‑1 (MQ=255)            aGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCcac                                                                                                                                         >  1:533910/1‑150 (MQ=255)            aGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCcac                                                                                                                                         >  2:817590/1‑150 (MQ=255)                       acaacctttATATTTTTGATTTGTTGCGGCCCGGCCGCGCCCCGTCGTTCGTTCCTTTT‑CCCTCGGCCTTCCCC‑GCCCCGCGATTTTCCCCCCCCC‑AAAAACTAAC‑CC‑GCCGGCGGGCGAAGAAAAGCAAAACCGCCACAGCGATGAGCg                                                                                                                              <  2:594850/143‑1 (MQ=255)                           cacTTATTTTTTTGATTTGTTGCGGGCCAGCCGCGATCCGGCGGTCGTCCTGTTT‑CCCTCGGCCTTCCCC‑GCCCCGCGTCTTTCCCCCCCCA‑AACACCAAAA‑CC‑GCTCGCTGGCGCAGGTAAGAAAAACCGCCACAGCGATg                                                                                                                                  <  2:83537/142‑1 (MQ=255)                               tataTTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGaa                                                                                                                      >  1:362274/1‑150 (MQ=255)                                 tatTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAAc                                                                                                                   >  2:422842/1‑151 (MQ=255)                                  atTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACt                                                                                                                  >  2:589149/1‑151 (MQ=255)                                      ttGATTTGTGGCGGCCCGGCCGCGTCCCGTCGGTCGTCCCTTTT‑CCCCCGCCCTTCCCC‑GCCCCGCGACTTTCCCCCCCCA‑AACAACAAAC‑CC‑GCCCGCGGGCGCAGAAAAGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTAc                                                                                                               <  1:817657/150‑1 (MQ=255)                                       tGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCg                                                                                                             >  1:449517/1‑151 (MQ=255)                                        gttatGTGGCAGCCCAGCCGCGTCCCGTGGGTCTTCCCTTTT‑CCCCCGCCCTTCCCC‑GACCGGCGATTTTCCCCCCCCA‑AACAAAAAAC‑CC‑GCCCGGGGGCCTAGGAAAGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTAc                                                                                                               <  2:81428/146‑1 (MQ=255)                                        gATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGc                                                                                                            >  1:136441/1‑151 (MQ=255)                                           atGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGcc                                                                                                           >  1:195907/1‑149 (MQ=255)                                              ttGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGa                                                                                                       >  1:175156/1‑150 (MQ=255)                                               tGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGaa                                                                                                      >  1:682564/1‑150 (MQ=255)                                               tGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGaa                                                                                                      >  1:102221/1‑150 (MQ=255)                                                    cccggTCGGGATCCGCCGGTC‑TTCCTTTTCGCCGC‑GCCTTTCCCGGCCCCGGGTTTTTTCCCCCCCA‑AACACCAAAC‑CC‑CCTCGGGGGCGCGGGAAGGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAAc                                                                                                    <  1:677719/143‑1 (MQ=255)                                                              aTCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTc                                                                                       >  1:406070/1‑150 (MQ=255)                                                              aTCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTc                                                                                       >  2:146875/1‑150 (MQ=255)                                                                     ggtcgTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTAtt                                                                               >  1:450602/1‑151 (MQ=255)                                                                       tcgTCCCTTTT‑CCCCCGCCTTTCCCC‑CCCCCGCGTTTTTCCCCCCCCA‑AACAACAAAC‑CC‑GCGCGCGGGCGCAGGAAAGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTa                                                                                 <  1:576095/147‑1 (MQ=255)                                                                                              tcccccccccGCCACTTTTCCCCCCCCAAACAAAAAAC‑CC‑CCTCGCGGGCGCGGTAAAGAAAAGCCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCtt                                                              <  2:638150/139‑1 (MQ=255)                                                                                              tCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGc                                                       >  2:276014/1‑151 (MQ=255)                                                                                               ccc‑gccccgcG‑CTTTCCCCCCCCC‑AAAAAAAAAACCC‑CCCCGCGGGCGAGGAAAAGAAAACCCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCa                                                      <  2:381897/151‑1 (MQ=255)                                                                                                    ccccGCGTTTTTCCCCCCCCC‑AACAACAAAC‑CC‑GCCCGCGGGCGCAGGAAAGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCa                                                   <  1:686595/149‑1 (MQ=255)                                                                                                     cccGCGTTTTTCCCCCCCCA‑AACAACAAAC‑CC‑CCCCGCGGGCGAAGTAAAAAAAACCCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCa                                                   <  2:547847/149‑1 (MQ=255)                                                                                                      cccgcgtttttCCCCCCCC‑AAAAAAAAAACCC‑GCTCGCGGGCGAGGGAAAAAAAACCCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCAt                                                     <  2:757537/140‑1 (MQ=255)                                                                                                         cgACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCAttt                                             >  2:129012/1‑151 (MQ=255)                                                                                                                  ccccccC‑AAAAACAAAC‑CC‑GCCCGCGGGCGCGGAAAAAAAAACCCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCtgatg                                    <  2:593093/151‑1 (MQ=255)                                                                                                                  ccccccC‑AA‑AACCAAA‑CCGGCCCGCTGGCGCAGGAAAAAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCtgatg                                    <  1:484295/151‑1 (MQ=255)                                                                                                                   cccccc‑AACAACAAAC‑CC‑GCCCGTTGGCGCAGGTAAAAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCtgatga                                   <  1:273510/151‑1 (MQ=255)                                                                                                                      tCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAAt                                >  2:143422/1‑151 (MQ=255)                                                                                                                      tCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAAt                                >  2:567324/1‑151 (MQ=255)                                                                                                                        c‑aacaaCTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAAtt                               >  1:59381/1‑150 (MQ=255)                                                                                                                          aacaatAAAC‑CC‑GCCCGCGGGCGCAGGAAACAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTTCTGATGAAAt                                <  1:210580/148‑1 (MQ=255)                                                                                                                          aaaaacAAAC‑CC‑GCCCGCTGGCGCAGGAAAGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAAtt                               <  1:378858/146‑1 (MQ=255)                                                                                                                            caacTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTc                            >  2:455234/1‑150 (MQ=255)                                                                                                                             aacTAAC‑CC‑GCGCGTTCGCGGAGGAAAAAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGaa                                  <  1:607198/143‑1 (MQ=255)                                                                                                                             aacTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAATCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCAt                          >  1:269898/1‑151 (MQ=255)                                                                                                                                    ccc‑gcccgcGGGCGAAGGAAAAAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTAc                       <  1:607887/147‑1 (MQ=255)                                                                                                                                     cccgccggtgggCGCGGGAAAAAAAACCCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTg                     <  1:716465/140‑1 (MQ=255)                                                                                                                                          ccggggcggcagaaaaGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTGCCgggg               <  1:646920/137‑1 (MQ=255)                                                                                                                                              gggcgcggaaaaGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTGCCGGGGCg             <  1:405558/139‑1 (MQ=255)                                                                                                                                              ggccgcAGGAAAGAAAACCCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTGCCgggg               <  1:62460/144‑1 (MQ=255)                                                                                                                                                       tAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTGCCGGGGCGTTAGAGGCAtt  >  1:458770/1‑151 (MQ=255)                                                                                                                                                       aaaGAAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTGCCGGGGCGTTAGAGGCAtt  <  1:112953/150‑1 (MQ=255)                                                                                                                                                           |                                                                                                                                                   ACTCGAGATGAAGCAGTCGATATCAACACTTATATTTTTGATATGTTGCAGGCCAGTCGCGATCCGTCGGTCGTTCCGTTT‑GCCTCGGCCTTTCCC‑GACCCGCGACTTTTCCCCCTCC‑AACAACTAAA‑CC‑GCTCGCTGGCGCAGGTAAGCAAAACCGCCACAGCGATGAGCGTGATTGAAAACTTACCGCCAGGAAACGCAGAACTGCGTCAGGCTATTGCTCGTCGCTATGCCTTACAGGGCATCACCATTTCTCCTGATGAAATTGTCATTACTGCCGGGGCGTTAGAGGCATT  >  NC_000913/1510246‑1510541

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑