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	100.0%	102.6 / NA	31	Q128* (CAG→TAG)	emrY	tripartite efflux pump membrane subunit EmrY
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (27/4);  total (27/4)

TTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGCTCCCAGAAAGC  >  NC_000913/2481565‑2482040                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                      tttGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGcc                                                                                                                                                                                                                                   >  1:353322/1‑251 (MQ=255)                           ttCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGTCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGActct                                                                                                                                                                                                          >  2:395166/1‑250 (MQ=255)                                          ttAAGCATATTGTCAGACCGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAGTTTATAACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCAAAATGC‑CAGACAAAATTTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGCCCCCGCCATTAACCCCTGAACAACTCTaaaaaaaataagccc                                                                                                                                                                                           >  2:1276/1‑241 (MQ=255)                                           tAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACAt                                                                                                                                                                                         >  1:133382/1‑251 (MQ=255)                                              gCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCa                                                                                                                                                                                       >  1:43460/1‑250 (MQ=255)                                                 tAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCa                                                                                                                                                                                       >  1:611063/1‑247 (MQ=255)                                                          taCGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCTTTAACCCCTGAACGACTCTAAAAACTATCAGCACATCCAGATTGGTcaat                                                                                                                                                                           >  2:491336/2‑247 (MQ=255)                                                            cGATAATCCCCATAGGGACATTGATTAAAACTATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAgg                                                                                                                                                                        >  1:512492/1‑251 (MQ=255)                                                             gATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAAATCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTATAAAAAATATCAGCACATCAAGATTGGTCGATatgc                                                                                                                                                                       >  2:296495/1‑248 (MQ=255)                                                               taccccccAGAGGAACATTAATAAAAAATACCCACCCCCAGCTAAA‑TTAACAAAAATAATACCCCCCAATAATCGCCCAACTTTTGGGAGGGAGAGTCGCGTTAATTGACAATAATCC‑CAAAAAAAATCTTCTTTTTTTGGGCGAATAATTCCTAAAAAAAAACCACTATGACAGGAAAATAAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCt                                                                                                                                                                      <  1:237872/246‑1 (MQ=255)                                                                         ggggACATTAATAAAAAATACCCACCCCCAGCAAAAGTTATCAAAAATAAACCCGCCAAATA‑TCGGCCCAAATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGAAAATGTTTTTTTTTCGGGCGAATAATTCCTTAAAAAAAACCTCTAGGACAGTGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATg                                                                                                                                                           <  1:17760/250‑1 (MQ=255)                                                                                                        cTAAAGTTATCACAAATATAACCGACCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTa                                                                                                                             >  1:457766/1‑250 (MQ=255)                                                                                                         tAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACCCATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTaa                                                                                                                            >  1:42596/1‑250 (MQ=255)                                                                                                                  caaaaaTATAACCACACAATA‑ACGCCCAACATATCGGCGCTATAACCATGGTCATTGACTATAA‑GCACAGAACAAATGTTTTTTTTTCTGGCGAATAATTCCTAAATAAAAAACTCTATGCCAGTGAAATTAACGCCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCt                                                                                                                   <  2:353322/247‑1 (MQ=255)                                                                                                                       atatAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTc                                                                                                             >  1:624775/1‑251 (MQ=255)                                                                                                                            aCCGCCCAATA‑TCGGCCAACATATCGTAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGAGACTGAAAGTAAAAATAATCTTAATTCGCCt                                                                                                         >  2:304746/1‑250 (MQ=255)                                                                                                                                   aaTA‑TCGCCCCACTTATCGGAGCAATAATCACGTTCTTTGACCATAATGC‑CAGAGCAATTTTTTTTTTTTCTGGCGAATATTTCCTTAATAAAAACCTCTAGAACAGTGAAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTtg                                                                                                 <  1:9202/251‑1 (MQ=255)                                                                                                                                    ata‑tCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTtgt                                                                                                >  2:79907/1‑251 (MQ=255)                                                                                                                                    ata‑tCGGCCCACATATCGGAGCGATAAACACGGTCATTGACCATAATGC‑CCTAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACACCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTATTtgt                                                                                                >  2:591856/1‑251 (MQ=255)                                                                                                                                                      ggAGCGATAATAACGGTCATTGAACATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGACATTAACCCCTGAACGActct                                                                                                                                                                                                          >  2:475804/1‑128 (MQ=255)                                                                                                                                                                  aCGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAAt                                                                   >  1:88893/1‑251 (MQ=255)                                                                                                                                                                   cGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATAGCAATg                                                                  >  1:267142/1‑251 (MQ=255)                                                                                                                                                                           gACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGc                                                          >  2:49078/1‑251 (MQ=255)                                                                                                                                                                                  aTGC‑CAGAGCGAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACATTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACCGCGAAAAAAAAGTGACTGAAAGTAAAACTAATCTTAATTAGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGAATTGGCATTTGCTACAcc                                                    >  2:479630/1‑250 (MQ=255)                                                                                                                                                                                       cAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACg                                               >  1:358749/1‑251 (MQ=255)                                                                                                                                                                                        agagCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACg                                               >  2:599231/1‑250 (MQ=255)                                                                                                                                                                                                        tttCTGGCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCgct                                                                                                                                                                           >  1:508420/1‑108 (MQ=255)                                                                                                                                                                                                             ggCGGATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGGAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTc                         >  2:152557/1‑251 (MQ=255)                                                                                                                                                                                                                ggATAATTCCTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGAACATCAAGCTTGGTCGATAGGATACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCAACACCAAACGAGGTGATCACCCAGGTGCCTTCGTc                      >  2:265270/1‑251 (MQ=255)                                                                                                                                                                                                                         cTTAATAATAAACTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGc             >  2:435763/1‑251 (MQ=255)                                                                                                                                                                                                                                    aCTCTATGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGCTCCCAGAAAGc  >  2:74599/1‑251 (MQ=255)                                                                                                                                                                                                                                         |                                                                                                                                                                                                                                                      TTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCATAGGGACATTGATTAAAAATATCCAACCCCAGCTAAAGTTATCACAAATATAACCGCCCAATA‑TCGGCCCACATATCGGAGCGATAATCACGGTCATTGACCATAATGC‑CAGAGCAAATGTTCTTTTTTCTGGCGGATAATTCCTTAATAATAAACTCTGTGACAGTGGAATTAACGGCCCCGCCATTAACCCCTGAACGACTCTAAAAAATATCAGCACATCAAGATTGGTCGATAGGCTACACATTAATGAAGACAGCGAAAAAAAAGTGACTGAAAGTAAAAATAATCTTAATTCGCCTATTCTTTGTGCCAACCTGCCAGTAACAGGGATCGCAATGGCATTTGCTACACCAAACGAGGTGATAACCCAGGTGCCTTCGTCTGTTGATGCTCCCAGAAAGC  >  NC_000913/2481565‑2482040

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: ‑