Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,481,795	G→A	Q128* (CAG→TAG)	emrY ←	tripartite efflux pump membrane subunit EmrY

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,481,795	0	G	A	96.5%	99.2 / ‑6.0	29	Q128* (CAG→TAG)	emrY	tripartite efflux pump membrane subunit EmrY
Reads supporting (aligned to +/- strand):  ref base G (0/1);  new base A (26/2);  total (26/3)
Fisher's exact test for biased strand distribution p-value = 1.03e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGCTCCCAGAAAGC  >  NC_000913/2481569‑2482040                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      aCCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGc                                                                                                                                                                                                                               <  2:7221/251‑1 (MQ=255)  ccGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGcc                                                                                                                                                                                                                              <  1:244371/251‑1 (MQ=255)                            ttAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTaaaaa                                                                                                                                                                                                     >  1:181558/1‑250 (MQ=255)                                 taagGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGAATCTAAAAAATATc                                                                                                                                                                                                >  2:31131/1‑250 (MQ=255)                                               aTGTCAGGACGATAATCCCCATAGGGACATTGTTTAAAAATATCCAACCCCAGCTAAAGTTATAACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACAATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCAATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTg                                                                                                                                                                                 >  1:469993/1‑251 (MQ=255)                                               aTGTCAGGACGATAATCCCCATAGGGACATTGATTAAAACTATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTg                                                                                                                                                                                 >  1:435219/1‑251 (MQ=255)                                               aTGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATACACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTTAACGACTCTAAAAAATATCAGCACATCAAGATTg                                                                                                                                                                                 >  1:216492/1‑251 (MQ=255)                                                       aCGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGAt                                                                                                                                                                           >  2:490873/1‑249 (MQ=255)                                                         gATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGc                                                                                                                                                                       >  1:304615/1‑251 (MQ=255)                                                           tAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCt                                                                                                                                                                      >  2:321797/1‑250 (MQ=255)                                                                          cATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGAc                                                                                                                                                      >  1:376135/1‑251 (MQ=255)                                                                              gataaaatacacccccccccAGCAAAAGTAAACACAAATACACCCCCCAAATACCCCCCCATATATGGGATCTATAATCACGTTCTTTAACCATAAGGCAAGAG‑AAATTTTTTTTTTTTTGGGTGGATAATTCCTAAAAAATACACTTTGTGAAAGGGAAATTACCGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGc                                                                                                                                                   <  1:315738/234‑1 (MQ=255)                                                                                   aaaaTATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGCTAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGaaaa                                                                                                                                              >  1:150390/1‑250 (MQ=255)                                                                                                            aTCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATACTCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAAATCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCCGAAAGACTCTAAAAAATATCAGCCCATCAAGATTGGTCGATAGGCTCCACATTAATGCAGACAGCGCAAAAAAAGTGACTGAAAGTAAAAATAATc                                                                                                                    >  2:116914/1‑251 (MQ=255)                                                                                                                       aaCCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCt                                                                                                         >  1:94603/1‑251 (MQ=255)                                                                                                                               aaTATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAGTAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTtg                                                                                                 >  1:164977/1‑251 (MQ=255)                                                                                                                                        ccACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCTATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCATAATTCGCCTATTCTTTGTGCCAACCt                                                                                        >  1:92295/1‑251 (MQ=255)                                                                                                                                                        tAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGCCAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTTTTTTTGCCAAACTGCCAGTAACAGGGAtt                                                                        >  2:180942/1‑250 (MQ=255)                                                                                                                                                          aTCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTg                                                                                                                                   >  1:310759/1‑190 (MQ=255)                                                                                                                                                                        ccATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCt                                                         >  1:41834/1‑250 (MQ=255)                                                                                                                                                                           tAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTacac                                                     >  1:126562/1‑251 (MQ=255)                                                                                                                                                                                       aaaTGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTg                                          >  2:482808/1‑250 (MQ=255)                                                                                                                                                                                              cTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGACTTAACGGCCCCGCCATTAACCCCTGAACGAct                                                                                                                                                                                                            >  2:37835/1‑81 (MQ=255)                                                                                                                                                                                                       gg‑CGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTc                         >  1:318036/1‑251 (MQ=255)                                                                                                                                                                                                            gATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCt                     >  1:161331/1‑251 (MQ=255)                                                                                                                                                                                                                aTTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGGGATAACCCAGGTGCCTTCGTCTGTTg                 >  2:484582/1‑251 (MQ=255)                                                                                                                                                                                                                     ttAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAACAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTGCACCAAAAGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGCt            >  1:172613/1‑251 (MQ=255)                                                                                                                                                                                                                        ataataaACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGCTccc         >  1:474493/1‑251 (MQ=255)                                                                                                                                                                                                                               aCTCTATGACAGTGGCATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATAAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAACCGAGGTGATAACCAAGGTGCCTTCGTCTGTTGATGCTCCCAGAAAGc  >  2:51411/1‑251 (MQ=255)                                                                                                                                                                                                                                    |                                                                                                                                                                                                                                                      ACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATATCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGCCAGAGCAAATGTTCTTTTTTCTGG‑CGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGCTCCCAGAAAGC  >  NC_000913/2481569‑2482040

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: ‑