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%	102.1 / NA	30	S60* (TCG→TAG)	waaU	lipopolysaccharide core biosynthesis
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base T (14/16);  total (14/16)

ATAGAGTAAGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCGAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCT  >  NC_000913/3798991‑3799260                                                                                                                                                |                                                                                                                               aTAGAGTAAGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACt                                                                                                                            >  7:40268/1‑148 (MQ=255)          gCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAAtt                                                                                                                  <  1:12108/149‑1 (MQ=255)           cATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTAATAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAAt                                                                                                                   >  1:115416/1‑147 (MQ=255)             tttCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAAt                                                                                                                   >  1:3748/1‑145 (MQ=255)               tCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATa                                                                                                                       >  1:40702/1‑139 (MQ=255)               tCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATa                                                                                                                       <  2:40702/139‑1 (MQ=255)                  aGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCAcc                                                                                                          <  6:101144/149‑1 (MQ=255)                         cGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTtta                                                                                                   <  2:18292/149‑1 (MQ=255)                          ggTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTttat                                                                                                  <  2:3748/149‑1 (MQ=255)                           gTTGATTCTTTAATACAGAACTCAAATATATTTTTATTAATAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTttatt                                                                                                 <  2:115416/149‑1 (MQ=255)                                      aaTACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTCCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGa                                                                                       <  8:81341/148‑1 (MQ=255)                                                                    agagagAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTttatt                                                                                                 >  5:118661/1‑108 (MQ=255)                                                                    agagagAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTttatt                                                                                                 <  6:118661/108‑1 (MQ=255)                                                                                     ccTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGAt                                                                        >  2:98134/1‑116 (MQ=255)                                                                                     ccTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGAt                                                                        <  1:98134/116‑1 (MQ=255)                                                                                     ccTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGattatt                                        >  6:106131/1‑148 (MQ=255)                                                                                           tATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGaata                                                                                    >  8:104918/1‑98 (MQ=255)                                                                                           tATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGaata                                                                                    <  7:104918/98‑1 (MQ=255)                                                                                             tttGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCAt                                                                                         >  5:99925/1‑91 (MQ=255)                                                                                             tttGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCAt                                                                                         <  6:99925/91‑1 (MQ=255)                                                                                                 tgAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATtatttatt                                    <  5:107837/140‑1 (MQ=255)                                                                                                 tgAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATtatttatt                                    >  6:107837/1‑140 (MQ=255)                                                                                                          ttATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGAt                                                        >  1:27781/1‑111 (MQ=255)                                                                                                          ttATTTTAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGAt                                                        <  2:27781/111‑1 (MQ=255)                                                                                                               ttAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAaaagaaa              <  5:106131/148‑1 (MQ=255)                                                                                                                tAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGa                                             >  6:56723/1‑116 (MQ=255)                                                                                                                tAACCCCTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGa                                             <  5:56723/116‑1 (MQ=255)                                                                                                                      cTTTACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAAtt       >  6:25037/1‑148 (MQ=255)                                                                                                                         tACTATAAAGTTCACGATAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAAt    <  5:25037/148‑1 (MQ=255)                                                                                                                                         aTAAATCTAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAATTTAATCt  >  3:106746/1‑134 (MQ=255)                                                                                                                                                |                                                                                                                               ATAGAGTAAGCATTTCAAGAAAACCGGTTGATTCTTTAATACAGAACTCAAATATATTTTTATTATTAGAGAGAAATTCCCCACCCTTTCTATTTGTGAGAAGAGTTATTTTAACCCCTTTACTATAAAGTTCACGATAAATCGAACTTAATACAATTAGATCACCAAGTTTATTATTATCATGAATAATAAGGCATGATTTAACTTGTGCTGGATCTGTAATTTGATTATTTATTTTATTACGAAATAAAAAAGAAAGGAAATTAATCT  >  NC_000913/3798991‑3799260

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑