Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	75,074	0	T	G	52.5%	39.7 / 56.0	40	N136T (AAC→ACC)	thiB	thiamine/thiamine pyrophosphate/thiamine monophosphate ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (6/13);  new base G (21/0);  total (27/13)
Fisher's exact test for biased strand distribution p-value = 2.25e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.98e-05

GCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAA  >  NC_000913/74945‑75222                                                                                                                                   |                                                                                                                                                        gCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCAt                                                                                                                                    >  2:179252/1‑151 (MQ=255)         gCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTTTCATAA‑aagaag                                                                                                                           >  2:666517/1‑151 (MQ=255)          ccATATCCTTTTTCCATCCATAGCAACAGACCCAGCCCCTGTGTACTGGTGCGCGGTTCCTGATAAATCGCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAgg                                                                                                                          <  1:410431/151‑1 (MQ=255)           cATAGCCTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGc                                                                                                                         <  1:152677/151‑1 (MQ=255)                            cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTTAGTTTTTTCTTTTTATAA‑AAAAAAGCGGAGTAGCCATAAT‑Caa                                                                                                       >  2:137575/1‑151 (MQ=255)                            cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGGTTTTTTTTGTTAAAA‑ACAAACGCGGAggtgcaatacataa                                                                                                        >  1:719818/1‑138 (MQ=255)                            cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTTTCATTA‑ACCAAGGCGAAGTAGGCATAAT‑Caa                                                                                                       >  1:63661/1‑151 (MQ=255)                            cATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTCTTTTCATAA‑ACGAAGGCGGAGAAGCCCTAAT‑Caa                                                                                                       >  2:575317/1‑151 (MQ=255)                              tAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAAc                                                                                                     <  2:297802/151‑1 (MQ=255)                                gCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTTTTATTA‑AAGAAGGCGCAGTAGCCCTAAT‑CAAAAgg                                                                                                   >  1:168269/1‑151 (MQ=255)                                 cAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACgg                                                                                                   <  1:199083/150‑1 (MQ=255)                                       ccccAGCCCCGGTGTACTGGGGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGaa                                                                                             <  1:713425/149‑1 (MQ=255)                                        cccAGCCCCGGTGTACTGGTGCGCGGTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGTTACGAAAg                                                                                           <  2:576270/151‑1 (MQ=255)                                        cccAGCCCCGGTGTACTGGTGCGCGGTTCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAg                                                                                           <  1:174223/151‑1 (MQ=255)                                               ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTTTTCTTTTTATAA‑ACAAAGGCGGAGGAGGCCTAAT‑CAAAACGTACGGAAatggtatt                                                                                    >  1:421429/1‑146 (MQ=255)                                               ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTTTTGTCATAA‑ACCAAGGCGGAGTAGGCATAAT‑CAAACGGGACGGAAATGTCatt                                                                                    >  1:50735/1‑151 (MQ=255)                                               ccGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑AAGAAGGCGGAGGAGGCCTAAT‑TAAAAGGGAAGAAAGTGTTatt                                                                                    >  1:347703/1‑151 (MQ=255)                                                  gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTTTTTTTGTTTTAATACAAAGG‑GGAGAAGCCATAAT‑CAAAAGGCACGGAAGGGGCattatt                                                                                 >  1:733061/1‑151 (MQ=255)                                                  gtgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑ACGAAAGCGGAGGAGCCCTAAT‑CAAACGGGAAGAAAATGTCattttt                                                                                 >  2:438233/1‑151 (MQ=255)                                                  gggtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTCTTGTTATAA‑AAAAAAGCGAAGAAGGCCAAAT‑CCAACAGTAAGGAAATGTCattatt                                                                                 >  1:74263/3‑151 (MQ=255)                                                   tgtACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTc                                                                                <  2:324459/151‑1 (MQ=255)                                                      aCTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGCGGGGTTTTTCTG‑TTGTTCTTTTTTTAA‑AAGAACGAGAAGCAAGCATAATACAAAAGGTGGGaaacggacttattacc                                                                               >  1:107911/1‑137 (MQ=255)                                                       cTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAgc                                                                            <  2:616767/151‑1 (MQ=255)                                                            gcgcGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTGTTATAA‑AAGAAAGCGAAGTAGCCATAAT‑CAAACGGGACGAAAGGGGCATTATTTCAGccg‑ccg                                                                      >  2:735332/1‑151 (MQ=255)                                                                 gATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTTAGTTTTTTTTTTTTATAA‑AAAAAAGGGGAGGAGCCCTAAT‑CAAAAGGGACGAAAGTGTGATTATTTCAGCCG‑CCgggga                                                                  >  1:447259/1‑148 (MQ=255)                                                                     cTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTTTCATAA‑AAGAAGGCGGAGGAGGCATAAT‑TAAAAGGTACGAAAATGTCATTATTTCAGCCC‑CCGGGGACGGTa                                                             >  2:572688/1‑151 (MQ=255)                                                                      tGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTCTTGTCATAA‑AAGAAGGCGAAGTAGCCATAAT‑CAAAAGGGACGAAAGTGTCATTATTTCAGCCGCCCGGGAAGGTTa                                                             >  2:69984/1‑151 (MQ=255)                                                                         tAAATCCCCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACgg                                                         <  1:222310/151‑1 (MQ=255)                                                                         tAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTTAGTTTTTTTTTGTCATAA‑ACCAAGGCGAAGTAGCCATAAT‑CAAACGGTACGGAAAGGTCATTATTTCAGCCG‑CCGGGGACGGTAACgg                                                         >  1:237036/1‑151 (MQ=255)                                                                         tAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACgg                                                         <  2:717402/151‑1 (MQ=255)                                                                           aaTCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTTTTTTTTTCCTAA‑AACAAGGCGGAGGAGGCATAAT‑TAAACGGGACGAAAGTGTCATTTTTTCAGCCG‑CCGGGGAAGTTAACGGCa                                                       >  1:548609/1‑151 (MQ=255)                                                                                       gTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑ACGAAAGCGCAGGAGCCATAAT‑CAAACGGTACGAAAGTGTCATTTTTTCACCCG‑CCGGGGACGTTAAAGGCATCCGCCGCcac                                            >  2:603809/1‑150 (MQ=255)                                                                                                gCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTTGTTTGTTTTTTTCATAA‑ACGAAAGAGAAGGAGACCTAAT‑CCAACGGGACGAAAGTGGCATTTTTCCAGCCG‑CCGGGGACGTTAACGGCATTCGCTGCCACACCGCctttt                                  >  2:340271/1‑150 (MQ=255)                                                                                                 ctctCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTTTTTTTGTCATAA‑AAGAAGGCGAAGGAGCCATAAT‑CAAAAGGGACGAAAAGGTCATTATTTCAGCCG‑CCGGGGAAGTTAACGGCATCCGCCGCCACACCCCcttttg                                 >  2:468852/1‑149 (MQ=255)                                                                                                 ctctCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑ACGAAGGCGGAGGAGCCCTAAT‑CAAAAGGGACGAAAGTGTCATTATTTCAGCCG‑CCGGGGACGGTAAAGGCATCCGCCGCCCCACCCCtttttg                                 >  2:335190/1‑149 (MQ=255)                                                                                                     cAACCAGTTCTTTCAGGCTTTGTGGC‑GGGGTTTTTAGTTTGTTTTTTTCATAA‑AAGAAAGCGAAGTAGCCATAAT‑TAAACGGGACGAAAGTGTCATTATTTCAGCCG‑CCGGGGACGTTAACGGCATCCCCTGCCCCACCGCTTTTTGCaaa                             >  2:572951/1‑151 (MQ=255)                                                                                                              cTTTCAGGCTTTGTGGC‑GGGGTTTTTTGGTTTTTCTTGTCATAA‑AAGAAGGCGGAGGAGCCCTAAT‑CAAACGGGACGGAAGTGTCATTTTTTCAACCG‑CCGGGGAAGTTTACGGCCTCCCCTGCCCCCCCCCCTTTTGCCAACAGTcccgg                    >  2:70136/1‑148 (MQ=255)                                                                                                                ttCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGttt                  <  2:447267/151‑1 (MQ=255)                                                                                                                      cTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTg             <  2:171240/150‑1 (MQ=255)                                                                                                                                 ggTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTaa  >  1:445050/1‑151 (MQ=255)                                                                                                                                   |                                                                                                                                                        GCGTCATCGCCATAGACTTTTTGCATCCATAGCAACAGACCCAGCCCCGGTGTACTGGTGCGCGGATCCTGATAAATCACCCGCCAGTTTTGATCGCTCTCAACCAGTTCTTTCAGGCTTTGTGGC‑GGGTTTTTCAGTTTGTTCTTGTCATAA‑ACGAAGGCGAAGTAGCCATAAT‑CAAACGGTACGAAAGTGTCATTATTCCAGCCG‑CCGGGAACGTTAACGGCATCCGCTGCCACACCGCTTTTGGCAAACAGTCCGGTTTTACTGGCGGCGTCTAA  >  NC_000913/74945‑75222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑