Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,412,898	0	C	T	41.1%	39.4 / 50.3	56	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (26/7);  new base T (0/23);  total (26/30)
Fisher's exact test for biased strand distribution p-value = 7.85e-10
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTT  >  NC_000913/3412750‑3413041                                                                                                                                                        |                                                                                                                                                 ccACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCtt                                                                                                                                                <  1:429334/151‑1 (MQ=255)   aCTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGt                                                                                                                                              >  2:183920/1‑151 (MQ=255)   aCTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGt                                                                                                                                              >  2:701894/1‑151 (MQ=255)     tAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGttt                                                                                                                                            >  2:820242/1‑151 (MQ=255)        aaCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTtata                                                                                                                                         <  2:187944/151‑1 (MQ=255)         aCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATaa                                                                                                                                        <  2:571067/151‑1 (MQ=255)            ggTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATaa                                                                                                                                        >  2:325870/1‑148 (MQ=255)             gTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGAt                                                                                                                                    <  1:738293/151‑1 (MQ=255)             gTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGAt                                                                                                                                    <  1:546912/151‑1 (MQ=255)                aaCTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCAt                                                                                                                                 >  1:632651/1‑151 (MQ=255)                 aCTGTGACGATCTGAATTTTCAGGACAGAATGTGAATTTACATGGCACTTAATTCATTCGTTTGATGAATTAATTTCGTTATTTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATTCGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCa                                                                                                                                  <  2:11469/149‑1 (MQ=255)                         gAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGcc                                                                                                                        >  2:267988/1‑150 (MQ=255)                               aaTTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTc                                                                                                                  >  1:837741/1‑150 (MQ=255)                               aaTTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTc                                                                                                                  >  2:866979/1‑150 (MQ=255)                                      aGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAAcc                                                                                                           >  1:804721/1‑150 (MQ=255)                                           aGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGtttt                                                                                                     >  1:168243/1‑151 (MQ=255)                                             aaTGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTg                                                                                                    >  2:805468/1‑150 (MQ=255)                                                 tgAATTTACATGACATTTATTTCATTCTTTTGATAAATTAATTTTTTTATGTTTCC‑ATCTGGCATGAACT‑TTCTT‑AATACTTTATCGACCAGGGGGGGGGTTTTTTTAAAAAGATAATAC‑CCCGCCATATTCATTAACCAGTTTTGAACa                                                                                                <  1:269585/150‑1 (MQ=255)                                                   attttACATACCATTTATTTCTTTTTTTTAATAATTTATTTTTGTTTTTTTTTC‑ATCTGGAATAAACT‑TTTTA‑AATACTTTACCGCCCAGGGGGGGGTTTTTTTTAAAAAAATAATAC‑CCCGCCATATTCATTAACCAGtttt                                                                                                     <  2:593736/141‑1 (MQ=255)                                                   aaTTTACATGCCATTTATTTCTTTCGTTTGATAAATTATTTTCTTTTTTTTTTC‑ATCGGGCATAAACA‑TTCTA‑AATCCTTTACCGACAGGGGGGGGGGTTTGTTTATAAAAATCAAAC‑CCCGCCATATTCATTAACCAGTTTTGAAc                                                                                                 <  1:199733/147‑1 (MQ=255)                                                     tttACATGACATTTAATTCATTCTTTTGATAAATTATTTTCTTTTTTTTTTC‑ATCGGGAATAAACT‑TTCTT‑AATCCGTTACCGACCGGGGGGGGGGTTTTTTAAAAAAAATAATAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTc                                                                                            <  1:720237/150‑1 (MQ=255)                                                     tttACATGAATTTTAATTAATGCTTTTGATAAATT‑ATTTTGTTTTGTTTTCTATTGGGTATAAACT‑TTTTT‑AATCCGTTAACAACCAAGGGGGGGTTTTTTTTAAAAAGAACAAAA‑CCCGCCATATTCATTAACCAGTTTTg                                                                                                    <  2:904107/142‑1 (MQ=255)                                                            gACATTTAATTCATTCTTTTGATAAATTATTTTCGTTATTTTTTC‑ATCTGGAATAAACT‑TTTTT‑AATCCTTTATCGACAAGGGGGGGGTTTTTTTAAAAAAGATCAAAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGaa                                                                                     <  2:243626/150‑1 (MQ=255)                                                                   aaTTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCAt                                                                             >  2:871756/1‑151 (MQ=255)                                                                     ttcattcGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATc                                                                            >  2:66152/1‑150 (MQ=255)                                                                      tcttttttttGAAAAATTATTTTCTTTATTTTTTC‑ATCTGGCATAAACA‑TTCTT‑AATCCTTTATCAACCAGAGGGGGGTTTTTTTTAAAAAAATCAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCa                                                                           <  2:435028/143‑1 (MQ=255)                                                                               tgatgaATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatc                                                                  >  1:543690/1‑150 (MQ=255)                                                                                 atgaTTTAATTTCGTTTTTTTTTC‑TTGTGGCATGAACT‑TTTTT‑AATATGTTATCGACCGGAGCGGGGGCTTTTTTAAAAAGAGCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatca                                                                 <  1:751819/149‑1 (MQ=255)                                                                                 ataaattatttTCTTTTTTTTTTC‑ATTTGGAAT‑AACATTTCTT‑ATCACTTTAGC‑AACAGGGGCGGGGTTTTTTTAAAAAAAACAAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatca                                                                 <  2:382581/146‑1 (MQ=255)                                                                                 aggaATTACTTTTGTTGTGTTTTC‑ATCTGGAAACATCT‑TATTT‑AATACTTTAGCGACCGGAGAGGGGTTTTGTTTATAAAGATCAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatca                                                                 <  1:162406/147‑1 (MQ=255)                                                                                  tgaATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatcatc                                                               >  1:739125/1‑150 (MQ=255)                                                                                    aattaattTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATcac                                                             >  1:382827/1‑150 (MQ=255)                                                                                    aattaattTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATcac                                                             >  1:539659/1‑150 (MQ=255)                                                                                      ttatttTCTTTATTTTTTC‑TTCTGACATAAACT‑TTTTT‑AATCCTTTATCGCCAAGAGGGGGGTTTTTTTTAAAAATATCAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATcac                                                             <  2:35568/148‑1 (MQ=255)                                                                                           tcgtttATTTTTTC‑A‑GTGGCAATAACA‑TTTTTAAATCCCTTATGACCCAGGGCGGGTGTGTGTAAAAAAAAATCAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                                      <  2:712116/146‑1 (MQ=255)                                                                                            ttttttttttttC‑ATCTGGAATGAACA‑TTCTT‑AACATTTTATCGACAAGGGGGGGGGTTTGTTTAAAAAAATCAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                                      <  2:854076/141‑1 (MQ=255)                                                                                            tcttttttttttC‑TTCTGGAAAAAACA‑TTCTT‑AACACTTTATCGACAAGAGCGGGGTTTTGTTTAAAAAGACAAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTa                                                     <  2:96966/142‑1 (MQ=255)                                                                                               tttttttttC‑TTTTGGAATAAACA‑TTCTA‑AACACTTTACCGAACAGAGGGGGGTTTTTTTAAAAAAGATAAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTa                                                     <  2:524444/142‑1 (MQ=255)                                                                                               ttATTTTTTC‑TGCTGGCATGAACA‑TTTTA‑AATATTTTTTCGACGAGAGCGGGGGTTTTTTTAAAAGGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAAt                                                  <  1:722853/150‑1 (MQ=255)                                                                                                ttttttttC‑TTCTGGAATAAACA‑TTTTT‑AATCCTTTAACGCCAAGGGGGGGGGTTTTTTTAAAAAAAACAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAAt                                                  <  2:26029/145‑1 (MQ=255)                                                                                                   tttttccaaatGGAATAAACA‑TTCTA‑AATACGTTATCGCCCATTGCGTGTTTTTTTTAAAAAATATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATc                                                 <  1:518021/138‑1 (MQ=255)                                                                                                      ttC‑ATCTGGCATGAACA‑TTCTT‑AATACTTTACCGACCAGGGGGGGGTTTTTTTTAAAAAAATAAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGtt                                           <  1:361556/150‑1 (MQ=255)                                                                                                              ggCATAAATT‑TTCTA‑AATACTTTATCAACCAGGGCGGGGGTTTTTTTATAAAAATCATAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGc                                     <  1:869884/149‑1 (MQ=255)                                                                                                              gaaataaaCT‑TTTTT‑AATCCTTTACCGCCCAGGGGGGGGTTTTTTTAAAAAAAATAATAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAttt                                       <  1:464262/141‑1 (MQ=255)                                                                                                                       a‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCtt                          >  1:240910/1‑151 (MQ=255)                                                                                                                         ttttt‑AATATTTTACCGCCCAGAGGGGGGGTTTTTTTAAAAAAATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCtt                          <  1:701943/147‑1 (MQ=255)                                                                                                                            tt‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCttgtt                       >  2:877042/1‑150 (MQ=255)                                                                                                                               aaTACGTTATCGACCAGAGCGGAGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCt                    >  2:519587/1‑151 (MQ=255)                                                                                                                                aTACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTg                   >  1:341688/1‑151 (MQ=255)                                                                                                                                  aCGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGac                 >  1:235771/1‑151 (MQ=255)                                                                                                                                   cGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGac                 >  1:5675/1‑150 (MQ=255)                                                                                                                                   cGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGac                 >  2:481792/1‑150 (MQ=255)                                                                                                                                     ttATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACg              >  2:688372/1‑151 (MQ=255)                                                                                                                                           acaagggggggggTTTTTTAAAAAAAATAAAAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGc         <  1:462734/142‑1 (MQ=255)                                                                                                                                              agagCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAt                                         >  1:760251/1‑115 (MQ=255)                                                                                                                                                 gggggggTTTTTTTAAAAAGAACATAC‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACtt  <  1:183944/149‑1 (MQ=255)                                                                                                                                                        |                                                                                                                                                 CCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAATTTCGTTATGTTTTC‑ATCTGGCATGAACA‑TTCTT‑AATACGTTATCGACCAGAGCGGGGGCTTGTTTATAAAGATCATAA‑CCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGCAATACTT  >  NC_000913/3412750‑3413041

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑