Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,481,804	0	G	A	39.4%	48.5 / 10.8	33	P125S (CCA→TCA)	emrY	putative multidrug efflux system
Reads supporting (aligned to +/- strand):  ref base G (19/1);  new base A (0/13);  total (19/14)
Fisher's exact test for biased strand distribution p-value = 2.44e-08
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCC  >  NC_000913/2481661‑2481936                                                                                                                                                |                                                                                                                                     aCCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAAc                                                                                                                               >  2:639956/1‑151 (MQ=255)        cTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCg                                                                                                                        >  2:449001/1‑151 (MQ=255)          aaaGTTATCACAAATATAACAGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGcc                                                                                                                           >  1:280725/1‑146 (MQ=255)             gTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCAtt                                                                                                                   >  2:529216/1‑151 (MQ=255)                ctCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAAc                                                                                                                >  1:133301/2‑151 (MQ=255)                  cacaAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAAccc                                                                                                              >  1:630486/1‑151 (MQ=255)                                         ggCCCACATATCGGAGCGATAATCACGGGCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATc                                                                                        >  1:468595/1‑150 (MQ=255)                                             cacaTATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcac                                                                                   >  2:642439/1‑151 (MQ=255)                                             cacaTATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCACCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGcac                                                                                   >  1:188264/1‑151 (MQ=255)                                                   tCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCa                                                                               >  1:323213/1‑149 (MQ=255)                                                           aTAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCg                                                                     >  2:552385/1‑151 (MQ=255)                                                                                  tGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGAc                                              >  2:204999/1‑151 (MQ=255)                                                                                      agagCAAATGTTTTTTTTTGGGGCGGATAATTATGAAAAAAAAAACACGGAGAGGAGGAAATAAAGGGCGCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACAACAAGATTGGTCGATAGGCTACACATTAATGAAGAc                                              <  1:685581/147‑1 (MQ=255)                                                                                      agagCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCg                                          >  1:622238/1‑151 (MQ=255)                                                                                      agaaaaattttttttttttCGGGGGAATAATTCCTAAAAAATAAACTCTGTGACGGTGAAATAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGAc                                              <  2:590789/134‑1 (MQ=255)                                                                                          aaaaTGTTTTTTTTTCTGGGGAATAATTCCTTAAAAAAAACCTCTGTGACAGTAAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaa                                       <  2:408640/149‑1 (MQ=255)                                                                                             aTGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaaaa                                    >  2:315873/1‑150 (MQ=255)                                                                                               gTTTTTTTTCCTGGAACATAATTCTTAAAAAAAAAACGGTGTGGTAAGGGATTTAACCGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAg                                 <  1:574118/151‑1 (MQ=255)                                                                                                 ttttttttCGGGGGGATACTTCATTAATAAAAACCTTTGAAACAGTGAAATTACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGt                                <  2:396664/148‑1 (MQ=255)                                                                                                 ttttttttCGGGCGAATAATTCCTAAATAAAAAACTCTGTGACAGGGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGt                                <  2:438953/148‑1 (MQ=255)                                                                                                 tCTTTTTTCAGGGAAATATTCCCTAAAAAAAAACCTAGGAGAAAGTGAATTAAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGt                                <  1:430266/150‑1 (MQ=255)                                                                                                           ggCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGt                      >  2:405442/1‑150 (MQ=255)                                                                                                                aTAATTCTTTAATAACAACTTCTGGGACAGGGAATTTACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTaaaaa                 <  2:446593/150‑1 (MQ=255)                                                                                                                aTAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAaat                >  2:478753/1‑151 (MQ=255)                                                                                                                      ccTAAAAAAAAAACTCTGTGACAGTGAAATAACCGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCt           <  2:106918/150‑1 (MQ=255)                                                                                                                        taaaaaataaCCTCTGTAAAAGAGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCtt          <  1:426222/144‑1 (MQ=255)                                                                                                                         taataataaACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAAt       >  2:579268/1‑151 (MQ=255)                                                                                                                         aaaaaaaaatctctGTAAGAGAGAAATAACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATc            <  1:496387/136‑1 (MQ=255)                                                                                                                          aaaaataaCCGCTGTAACATTGAAATTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTa         <  1:430885/145‑1 (MQ=255)                                                                                                                             aaaaacctctGTGACGGTGAAATAATCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGc   <  2:487018/145‑1 (MQ=255)                                                                                                                             aaaaacctctGTGACAGTGAAATTACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCg    <  2:514979/144‑1 (MQ=255)                                                                                                                              ataaACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGcc  >  2:426685/1‑151 (MQ=255)                                                                                                                                aaaCTCTGTGACAGTGGAATTAACGGCCCCGCCATTACCCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGATAAAAAAGTGACTGAACGTAAAAATAATCTTAATTc     >  1:656459/1‑146 (MQ=255)                                                                                                                                                |                                                                                                                                     ACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCC  >  NC_000913/2481661‑2481936

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑