Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,481,804	0	G	A	44.4%	61.2 / 26.9	54	P125S (CCA→TCA)	emrY	putative multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base G (26/4);  new base A (0/24);  total (26/28)
Fisher's exact test for biased strand distribution p-value = 1.48e-11
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTT  >  NC_000913/2481657‑2481944                                                                                                                                                       |                                                                                                                                              tCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAAt                                                                                                                                            >  1:865520/1‑151 (MQ=255)   cAACCCCAGCTAAAGTTATCACAAATATAACCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTa                                                                                                                                          <  2:308575/151‑1 (MQ=255)              aaaGTTATCACAAATATAACCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGcc                                                                                                                              >  2:143767/1‑151 (MQ=255)               aaGTTATCACAAATATAACCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGcc                                                                                                                              >  1:423130/1‑150 (MQ=255)                  ttaaccaaaaaaaaaCCCCCCAAATACCGCCCCACATATCGGAGAAAAAATCACGTTCATTGACAATAATGCAAGAGAAAATGTTCTTTTTTCTGGCGGATAATCCCTA‑AAAAAAAAC‑CTCTGTGACAGGGAAATAAACGG‑CCCCGCCAt                                                                                                                            <  2:406403/137‑1 (MQ=255)                             ataACCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGATCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACg                                                                                                               >  2:832698/1‑151 (MQ=255)                               aaCCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGAc                                                                                                             >  2:541811/1‑151 (MQ=255)                                  cGCCA‑AATACCGGCCAAAATACGGGAGCGAAAATCACGGTCATTGCCCATAATCCCAGAGAAATTTTTTTTTTTTCGGGGGAATATTTCTTA‑AATAAAAAC‑CCCTGGGACAGGGAATTTACCGG‑CCCCGCCATTAACCCCTGAACGAct                                                                                                            <  1:806730/149‑1 (MQ=255)                                          tatCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAat                                                                                                   >  1:502382/1‑151 (MQ=255)                                             cgccccACATATCGGAGCGATAACCACGGTCATTGACCATAATGCCAGAGAAAATTTTTTTTTTTCGGGCGGATAATTCCTT‑AAAAATAAA‑CTCTGTGAAAGAAAAATAACCGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAata                                                                                                  <  2:89225/146‑1 (MQ=255)                                             cGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATc                                                                                                >  1:462032/1‑151 (MQ=255)                                              ggCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATc                                                                                                >  1:717897/1‑150 (MQ=255)                                              ggCCCACATATCGGAGCAATAACCCCGGTCTTTGACCATAAGGCAAGAGCAAATTTTCTTTTTTCGGGCGGATAATTCTTA‑AAAAAAAAC‑CTCTGTGACAGTGAAATAAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAatat                                                                                                 <  1:610026/149‑1 (MQ=255)                                                   acaTATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcac                                                                                           >  1:148790/1‑150 (MQ=255)                                                     atatGGGAGCTATAATCACGGTCATTGACAAAAATGCAAGAGAAATTTTTTTTTTTTCTGGGGAATAATTCCTT‑AAAAAAAAA‑CTCTGTGAAAGGAAAATAAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGca                                                                                            <  2:318886/147‑1 (MQ=255)                                                       agcGGAGCGTAAATCACGTTCATAGACCATAAAGCCAGACAAATTTTTTTTTTTTCTGG‑AAATTATTCCTT‑AAAAAAAAACCCCTGTAACAGTGGAATTACCGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACAt                                                                                         <  1:368376/146‑1 (MQ=255)                                                         cGGAGCGATAATCACGGTCATTGACCATAATGCCAGCGCAAATGTTCTTTTTTCTTGCGGATAATTCCTT‑AATAATAAA‑CTCTGAGTCAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAACAAAATTAGCACATCa                                                                                       >  2:853203/1‑148 (MQ=255)                                                           gAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGAtt                                                                                  >  2:605201/1‑151 (MQ=255)                                                           gAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTCCTTTTTTCTGGTGGGTAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGAtt                                                                                  >  2:871167/1‑151 (MQ=255)                                                               attatccccGGTCATTGCCAATAACGCAAGAAAAATTTTTTTTTTTTCTGGCGTATAATCCTTT‑AATAATAAG‑CTCTGTGAGGGTGAATTTAACGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGAt                                                                                   <  1:474578/138‑1 (MQ=255)                                                                  actcagggtattggACCATAGTCCAAGAAAAAATTTTTTTTTTTCTGGGGAATAATTCCTA‑AATAAAAAC‑CTCGGTGAAAGTGAAATTACCGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTg                                                                                 <  1:514100/132‑1 (MQ=255)                                                                       cgctCATGGACTATAATCAGAGAACAATTTTTTTTTTTTTCGGTGGTTATTACCTT‑AATAATAAG‑CTGGGAAAAGGTGAAATTAACCG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAg                                                                         <  1:546469/145‑1 (MQ=255)                                                                                accaaaagcccAGAAAAATTGTTTTTTTTCCGGGGGGATAATTCATA‑AATAAAAAC‑CTCGGTGAAAGATAAATAAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTaa                                                             <  2:75685/142‑1 (MQ=255)                                                                                acaaTAATGCAAGAGCAATTTTTTTTTTTCCGGGCGGATATTTCTTA‑AATAATAAA‑CCCGGGGAAAGTGAAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACAtt                                                               <  2:41443/146‑1 (MQ=255)                                                                                      aTGCCAGAGCAAATTTTTTTTTTTCTGGCGGAAAATTCCTA‑AAAAAAAAC‑CTCTGGGACAGTGGAATTAACGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGa                                                       <  1:106087/151‑1 (MQ=255)                                                                                        gCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGAc                                                      >  2:765688/1‑150 (MQ=255)                                                                                         ccAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGAc                                                      >  1:808242/1‑149 (MQ=255)                                                                                              gCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaa                                                >  2:159536/1‑150 (MQ=255)                                                                                               aaaaTGTTTTTTTTTCGGGCGGATAATTCCTA‑AAAAATAAC‑CTCTGTGCCAGTGAAATTAACGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaa                                                <  1:616705/148‑1 (MQ=255)                                                                                                aattttttttttttCGGGCGAATAATTCTTA‑AAAAAAAAA‑CTCTGTGACAGTGAAATTACCGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaa                                              <  1:72408/142‑1 (MQ=255)                                                                                                aaaTTTTTTTTTTTCTGGGGTATAATTCTTA‑AAAAAAAAC‑CTCTGTGAAAGGAAAATTAACCG‑CCCCGCCATTAACCCCCGAACGAATCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaa                                             <  2:643071/151‑1 (MQ=255)                                                                                                aaaTTTTTTTTTTTCGGGC‑GAAAATTTCTT‑AAAAAAAAACCTCGGGAACAGGGAAATAAACGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACa                                                     <  1:364241/143‑1 (MQ=255)                                                                                                aaaTGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaa                                              >  1:553710/1‑150 (MQ=255)                                                                                                    gTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaaaa                                           >  2:79716/1‑149 (MQ=255)                                                                                                       cTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTg                                       >  2:5693/1‑150 (MQ=255)                                                                                                        ttttttCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGAc                                     >  2:57231/1‑151 (MQ=255)                                                                                                                ggCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGt                              >  2:492608/1‑150 (MQ=255)                                                                                                                ggCGAATAATTCTTT‑AAAAAAAAA‑CTCTGAGAAAGTGAAATCACCGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTa                             <  2:855220/151‑1 (MQ=255)                                                                                                                ggCGAATAATTCTTA‑AAAAAAAAA‑CTCGGTAAAAGGAAAATTACCGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAg                               <  2:322701/149‑1 (MQ=255)                                                                                                                 ggggaataTTCCTTAAAAAAAAAA‑CTTTGGGACAGGAAAATTACCCA‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTa                             <  2:502296/144‑1 (MQ=255)                                                                                                                    gATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTaaaa                          >  1:924024/1‑150 (MQ=255)                                                                                                                     aTAATTCCTA‑AAAAAAAAA‑CTCTGTGACAGTGAAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaat                        <  1:172564/151‑1 (MQ=255)                                                                                                                       atttCCTT‑AAAAAAAAA‑CTCTGTAAAAGAGAAATAACCGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaat                        <  2:679491/147‑1 (MQ=255)                                                                                                                         ttCTTT‑AAAAAAAAC‑CTCGGAGACAGTGAAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaat                        <  1:908710/147‑1 (MQ=255)                                                                                                                         ctCCTT‑AAAAACAAA‑CTCTGGAACAG‑AAAATTAACGGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTaaaaa                         <  1:508859/145‑1 (MQ=255)                                                                                                                           ccTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCtt                  >  2:781912/1‑151 (MQ=255)                                                                                                                                aataataaA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAAtt              >  1:303615/1‑151 (MQ=255)                                                                                                                                aaaaataaC‑CTCTGTGACAGTAAAATAACGGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAAt               <  1:668932/147‑1 (MQ=255)                                                                                                                                  aaaaaaa‑CTCTGTGAAAGTGAAATTAACGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCg            <  2:596188/147‑1 (MQ=255)                                                                                                                                    ataaA‑CCCGGTGAGAGAGGAATAAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGcc          <  1:909929/151‑1 (MQ=255)                                                                                                                                          ctctGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTc     >  2:191378/1‑151 (MQ=255)                                                                                                                                           tctGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCt    >  2:683555/1‑151 (MQ=255)                                                                                                                                            ctGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCtt   >  2:507437/1‑151 (MQ=255)                                                                                                                                                 aCAGAGAAATAAACGC‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCttt  <  2:152473/147‑1 (MQ=255)                                                                                                                                                       |                                                                                                                                              TCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCC‑AATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTT‑AATAATAAA‑CTCTGTGACAGTGGAATTAACGG‑CCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTT  >  NC_000913/2481657‑2481944

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑