Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,799,134	G→T	S60* (TCG→TAG)	waaU ←	lipopolysaccharide core biosynthesis

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,799,134	0	G	T	100.0%	101.3 / NA	30	S60* (TCG→TAG)	waaU	lipopolysaccharide core biosynthesis
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (16/14);  total (16/14)

AGAGTAAGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCGAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCTTGATTTTGTTTATATAAA  >  NC_000913/3798993‑3799278                                                                                                                                              |                                                                                                                                                 agagTAAGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTaa                                                                                                                                           >  6:9179/1‑149 (MQ=255)   agTAAGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTATATTTGTGAGAAGAGTTATTTTAACCCATTTAATATAAAGTTCACGATAAATCTAAATTAAt                                                                                                                                          >  5:57169/1‑148 (MQ=255)       aGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACaa                                                                                                                                      <  6:50892/148‑1 (MQ=255)           tttCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGa                                                                                                                                 <  5:9179/149‑1 (MQ=255)                  aaaaCCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCAcc                                                                                                                            >  6:51611/1‑147 (MQ=255)                    aaCCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGt                                                                                                                        <  5:51611/149‑1 (MQ=255)                         gTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTaa                                                                                                                                           <  1:79626/125‑1 (MQ=255)                         gTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTaa                                                                                                                                           >  2:79626/1‑125 (MQ=255)                              ttCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTtattattat                                                                                                              >  1:134536/1‑149 (MQ=255)                                                       tttttAGTATTAGAGAGAAATTCCCCACCCGTTCTCTTTCTGAGAAGAGTTACCTTCACGCCGTTACTCTAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGGCTATTATTATCATGAATAATACGGCATGATTTAAc                                                                                     <  8:91385/149‑1 (MQ=255)                                                              tattaGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTtattattat                                                                                                              <  8:31141/117‑1 (MQ=255)                                                              tattaGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTtattattat                                                                                                              >  7:31141/1‑117 (MQ=255)                                                                ttaGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTg                                                                             >  5:99544/1‑148 (MQ=255)                                                                   gagagaAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTa                                                                                                                                   <  1:80308/91‑1 (MQ=255)                                                                   gagagaAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTa                                                                                                                                   >  2:80308/1‑91 (MQ=255)                                                                   gagagaAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGAt                                                                          <  6:99544/148‑1 (MQ=255)                                                                    agagaAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCt                                                                        >  4:54421/1‑149 (MQ=255)                                                                    agagaAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCt                                                                        >  1:62036/1‑149 (MQ=255)                                                                           ttCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAAttt                                                                 <  6:57169/149‑1 (MQ=255)                                                                                         tATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTAtttatttta                                                   >  8:14057/1‑149 (MQ=255)                                                                                            ttGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATttattttatt                                                 <  2:62036/148‑1 (MQ=255)                                                                                             tgtgAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTttatta                                                <  2:134536/148‑1 (MQ=255)                                                                                                           ttttAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGa                                                                           >  6:46636/1‑107 (MQ=255)                                                                                                               aaCCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAgg                              >  5:79815/1‑148 (MQ=255)                                                                                                                 ccccTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGaaa                           >  3:122882/1‑149 (MQ=255)                                                                                                                               aGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGTCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCTTGAtttt             <  4:122882/149‑1 (MQ=255)                                                                                                                                       aTAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCTTGATTTTGTTtatat     <  6:79815/149‑1 (MQ=255)                                                                                                                                       aTAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCTTGATTTTGTTtata      >  7:120703/1‑148 (MQ=255)                                                                                                                                       aTAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCTTGATTTTGTTtata      >  8:104796/1‑148 (MQ=255)                                                                                                                                          aaTCTAAATTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCTTGATTTTGTTTATATaaa  <  7:14057/149‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                 AGAGTAAGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCGAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCTTGATTTTGTTTATATAAA  >  NC_000913/3798993‑3799278

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑