Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,481,400	T→A	S259S (TCA→TCT)	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	2,481,400	0	T	A	100.0%	61.4 / NA	18	S259S (TCA→TCT)	emrY	tripartite efflux pump membrane subunit EmrY
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base A (6/12);  total (6/12)

AACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTGGCATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCTGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCAT  >  NC_000913/2481158‑2481636                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                             aacaacCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTGGCATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCg                                                                                                                                                                                                                                       <  1:156016/250‑1 (MQ=255)   caacCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTGGAATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATAATCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACt                                                                                                                                                                                                                                    >  1:36783/1‑251 (MQ=255)                   ttgttgCCATAACGTCCTATCAAAGGTGAAATTAATAGTGGCATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCAGTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAATGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTTAAGTTACGGGACTTAAACAAACTCAGATCAAGAATCGGGTTCTCAGAGTTCGACTCCCAAATGACTAAag                                                                                                                                                                                                                     <  2:86508/250‑1 (MQ=255)                                     aTCAAAGGTGAAATTAATAGGGGCATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGa                                                                                                                                                                                                  <  1:246590/251‑1 (MQ=255)                                               aaaTTAATAGTGGCATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGtt                                                                                                                                                                                        <  1:206812/251‑1 (MQ=255)                                                          ggCATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAAtattatta                                                                                                                                                                              <  2:52338/250‑1 (MQ=255)                                                                                 aGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATcc                                                                                                                                                       >  2:105929/1‑250 (MQ=255)                                                                                    aaGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATGACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGAt                                                                                                                                                   <  1:110059/251‑1 (MQ=255)                                                                                      gTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATcg                                                                                                                                                 <  1:56842/251‑1 (MQ=255)                                                                                                                                              aCGATCGCTCCAGAGTAAAATAAATACGCGCATGAGATACTCACACTACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTc                                                                                           >  1:110612/1‑249 (MQ=255)                                                                                                                                                gATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTc                                                                                       >  1:129276/1‑251 (MQ=255)                                                                                                                                                                          cgcATGTGATACTCACAATACCAATGGTGAAGTTACGTGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGaa                                                             <  2:139307/251‑1 (MQ=255)                                                                                                                                                                               gtgATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATGTTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGtctc                                                        <  2:184267/251‑1 (MQ=255)                                                                                                                                                                                                   ggTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTtaagta                                    <  2:219446/251‑1 (MQ=255)                                                                                                                                                                                                      gAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTGAAGTAAgg                                 <  1:1367/251‑1 (MQ=255)                                                                                                                                                                                                             cGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGc                           >  1:114140/1‑250 (MQ=255)                                                                                                                                                                                                                    tAAACAAACTGAGATCAAGAATCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGGTAAGCATAATGt                    <  1:80735/250‑1 (MQ=255)                                                                                                                                                                                                                                       aaTCGGGTTCTCAGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCAt  >  1:237931/1‑249 (MQ=255)                                                                                                                                                                                                                                                   |                                                                                                                                                                                                                                             AACAACCGCATGTCTATTTTGTTGCCATAACGTCCTATCAAAGGTGAAATTAATAGTGGCATGATGCCGATGGGCGCATAAGCAAGTCCGGCCCATATCGCATTATACCCCATCGTTTCCTGGAGTAACTGCGGCATAAGGACGATCGCTCCAGAGTAAAATAAATACGCGCATGTGATACTCACAATACCAATGGTGAAGTTACGGGACTTAAACAAACTGAGATCAAGAATCGGGTTCTCTGAGGTCGACTCCCAAATGACTAAAGAGATCAGAGAAATAACTGATACTACTGTTAATATTATTATTGTACTCGAGTTGAACCAATCCAGATCGCGCCCTTTATCAAGCATAATTTGCAAGCCACCAACACCGAGCACTAACAGGGTCAGTCCTGGTAGATTCATTTTGACCGGTGAAGTCTCAGTTTCTCTTCCTTTAAGTAAGGTTAAGCATAATGTCAGGACGATAATCCCCAT  >  NC_000913/2481158‑2481636

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑