Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,412,898	0	C	T	39.1%	53.6 / 27.6	48	A190T (GCC→ACC)	acrS	acrAB operon transcriptional repressor
Reads supporting (aligned to +/- strand):  ref base C (23/5);  new base T (0/18);  total (23/25)
Fisher's exact test for biased strand distribution p-value = 2.39e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATCCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGC  >  NC_000913/3412748‑3413034                                                                                                                                                          |                                                                                                                                          aTCCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGc                                                                                                                                           >  2:617455/1‑151 (MQ=255)  tCCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCt                                                                                                                                          >  2:1580/1‑151 (MQ=255)        aaaaCTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGttt                                                                                                                                     <  1:399754/150‑1 (MQ=255)               gTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGAt                                                                                                                            <  2:378495/151‑1 (MQ=255)                  aaCTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCAt                                                                                                                         <  2:96189/151‑1 (MQ=255)                  aaCTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCAt                                                                                                                         >  2:672481/1‑151 (MQ=255)                   aCTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATa                                                                                                                        <  1:403180/151‑1 (MQ=255)                         aCGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGc                                                                                                                  >  2:440082/1‑151 (MQ=255)                          cGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGcc                                                                                                                 <  2:568806/151‑1 (MQ=255)                           gAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGcc                                                                                                                 >  1:518876/1‑150 (MQ=255)                                gAATTTTCAGAACAAAATGTGAATTTACATGACACTTAATTCATTCTTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATCCGTTATCGACCAGAGCGGGGGTTTGTTT‑ATAAAGATCATAACCCGCCatat                                                                                                             <  1:134778/149‑1 (MQ=255)                                 aaTTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTc                                                                                                           >  2:541823/1‑150 (MQ=255)                                         ggACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAAcc                                                                                                    >  1:529177/1‑149 (MQ=255)                                              gAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGtttt                                                                                              >  1:227133/1‑150 (MQ=255)                                               aaTGTAAATTTACATGACATTTAATTCTTTCTTTTGATAAATTAT‑TTTGTTTTTTTTT‑TCTTCTGGCAAAAAC‑ATTTTTAATACTTTATCGCCCAGGGCGGGGGTTTTTTT‑AAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTg                                                                                             <  2:637647/150‑1 (MQ=255)                                                        ttacattacaTTAAATTCTTTTTTTTAATAAATAAT‑TGTCGTTTTGTTT‑TTACCTGGAATAAAC‑ATTTTAAATAC‑TTAACCATCTGGGGGGGGGGTTTTTTAAAAAAGAACAGAACCCGCCATATTCATTAACCAGTTTTGAACAAt                                                                                       <  1:66021/147‑1 (MQ=255)                                                        ttACATGACATTTAATTCATTCTTTTGATAAATTAA‑TTTCTTTTTTTTT‑TCATCTGGCATGAAC‑ATTCTTAATCCGTTATCGACCAGGGCGGGGGTTTTTTT‑AAAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTcc                                                                                    <  2:156376/150‑1 (MQ=255)                                                          aCATGCCATTTATTTCATTGTTTTGAGGAATTAA‑TTTC‑TTTTGTTTATCATCTGGCATGCAC‑ATTTTTAATTCATTATCGACCAAGGCGGGGGGTTTTTT‑AAAATTACCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCg                                                                                   <  1:576596/149‑1 (MQ=255)                                                           cATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTg                                                                                >  2:332862/1‑151 (MQ=255)                                                            aTGACTTTTAATTCATTGGTTTGATGAATTAT‑TTTCTTTTTGTTT‑TCATCTGGAATAAAC‑ATTTTAAATACTTTACCGACCAGGGGGGGGGTTTGTTA‑AAAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCg                                                                                   <  2:332335/147‑1 (MQ=255)                                                                ctctaattttattgttttGAT‑AATTAATTTTCGTTATGTTT‑CCA‑GTGGAATTAACTATTCTTAACATGTTACCCCCCAGGGGGGGGGTTTTTTA‑AAAAATCTAATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAgg                                                                            <  1:44157/135‑1 (MQ=255)                                                                cctttATTTCATTCTTTTGATTATTTAT‑TTTCGTTTTTTTT‑TCTTATGGCATAAAC‑ATTCTAAATCCTTTACCGACAAGGGGGGGGGTTTTTTT‑AAAAAAAACAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAg                                                                             <  2:658125/146‑1 (MQ=255)                                                                   ttAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCAcc                                                                        >  2:442022/1‑151 (MQ=255)                                                                         cattcGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaat                                                                  >  1:307518/1‑151 (MQ=255)                                                                            ttttttAATAAATTAT‑TTTCTTTTTTTTT‑CCATCTGGAATGAAA‑ATTTTAAATCCGTTCTCCACCAGAGCGGGGGTTTTTTA‑AAAAAAATAAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaataa                                                                <  2:175078/147‑1 (MQ=255)                                                                                ttGATAAATTAT‑TTTCTTTTTTTTT‑TCATCTGGCATAAAC‑ATTCTTAATACTTTACCGCCCAGGGGGGGGGTTTTTTT‑AAAAAGATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCaataataat                                                            <  2:435893/150‑1 (MQ=255)                                                                                   atgaATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatcat                                                         >  1:667282/1‑150 (MQ=255)                                                                                      aattat‑ttTCTTTTTTTTT‑TCATCGGGAATAAAC‑ATTTTTAATCCTTTATCGACAAGGGGGGGGGTTTGTTA‑AAAAAAATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAatcatc                                                        <  2:287957/148‑1 (MQ=255)                                                                                      aattat‑ttTCTTTATTTTT‑TCATCTGAAAAGAAC‑ATTCTTAATATTTTATCGACAAGGGGGGGGTTTTTTTA‑AAAAAGATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATcac                                                      <  2:10592/150‑1 (MQ=255)                                                                                        ttat‑ttTCTTTTTTTTT‑TCTTCTGGCATGAAC‑TTTTTTAATACTTTACCGCCCAGAGGGGGGGTTTTTTT‑ATAAAAATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCacaa                                                    <  2:276609/150‑1 (MQ=255)                                                                                        ttaa‑ttTTTTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTACCGACCAGAGGGGGGGTTTGTTT‑ATAAAAATCATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATcac                                                      <  2:598580/148‑1 (MQ=255)                                                                                           attttCTTTATTTTT‑TCATCTGGCATAAAC‑ATTCTTAATACTTTATCGACCAGGGCGGGGTTTTTTTT‑ATAAAGATCAAAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCacaaca                                                  <  2:201566/148‑1 (MQ=255)                                                                                             tttCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                               >  2:521483/1‑151 (MQ=255)                                                                                              ttCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCt                                               >  1:578466/1‑150 (MQ=255)                                                                                                  ttATTTTT‑TCATCTGCCATAAAC‑ATTTTAAATACATTATCGCCCAGAGGGGGGGTTTTTTA‑AAAAAGAACATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTaa                                             <  1:623555/148‑1 (MQ=255)                                                                                                      gTTT‑CCATCGGGCAGAAAC‑TTTCTAAAGACGTGAGCGACAAGGGGGGGGGTTTTTTT‑AAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTa                                              <  2:686792/143‑1 (MQ=255)                                                                                                       ttt‑tCATCTGATATAAAC‑ATTTTTATTCCTTTACCGACCAGGGGGGGTTTTTGTTT‑ATAAAGATAATACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGa                                        <  2:588218/148‑1 (MQ=255)                                                                                                            cattggaaaagAAC‑ATTTTTAATACTTTATCGACAGGAGGGGGGTTTTTTTT‑AAAAAGACCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAt                                  <  1:438587/140‑1 (MQ=255)                                                                                                            cATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTAtt                                 >  2:522979/1‑151 (MQ=255)                                                                                                              tCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTg                               >  1:253517/1‑151 (MQ=255)                                                                                                                   cATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTac                           >  2:589583/1‑150 (MQ=255)                                                                                                                      gacc‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTAcaca                        >  1:627238/4‑150 (MQ=255)                                                                                                                           aTTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCtt                   >  2:382073/1‑151 (MQ=255)                                                                                                                                 aaTTCGTTATCGCCCAGGGGGGGGTTTTTTTT‑AAAAAGATCAAACCCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGc              <  2:687227/150‑1 (MQ=255)                                                                                                                                 aaTACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCt             >  2:497380/1‑151 (MQ=255)                                                                                                                                  aTACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTg            >  2:383288/1‑151 (MQ=255)                                                                                                                                        tATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGc      >  2:417638/1‑151 (MQ=255)                                                                                                                                        tATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGc      >  2:388271/1‑151 (MQ=255)                                                                                                                                             aCCAGCGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGc  >  1:43279/1‑150 (MQ=255)                                                                                                                                                          |                                                                                                                                          ATCCACTAAAACTGGTTAACTGTGACGAACTGAATTTTCAGGACAGAATGTGAATTTACATGACACTTAATTCATTCGTTTGATGAATTAA‑TTTCGTTATGTTT‑TCATCTGGCATGAAC‑ATTCTTAATACGTTATCGACCAGAGCGGGGGCTTGTTT‑ATAAAGATCATAACCCGCCATATTCATTAACCAGTTTTGAACAATTCCGCTGAAGGCACCATCAATAATAATCATCACAACATCTAAATCGAGGTTATTTGCTACACAACCTTGTTGCTGACACGCCTGC  >  NC_000913/3412748‑3413034

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: ‑