Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,599,363	T→C	H99R (CAC→CGC)	livJ ←	branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,599,363	0	T	C	100.0%	117.4 / NA	35	H99R (CAC→CGC)	livJ	branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (25/10);  total (25/10)

CCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCG  >  NC_000913/3599229‑3599498                                                                                                                                       |                                                                                                                                        ccAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCa                                                                                                                                    <  1:726113/140‑1 (MQ=255)       cGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATcaca                                                                                                                              <  2:499245/140‑1 (MQ=255)         gtggtgCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACata                                                                                                                            >  1:337672/1‑140 (MQ=255)          tggtgCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACatat                                                                                                                           >  1:462736/1‑140 (MQ=255)                   ggATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCcg                                                                                                                  <  2:34493/140‑1 (MQ=255)                    gATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCcgt                                                                                                                 >  1:1118088/1‑140 (MQ=255)                         gCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTa                                                                                                            >  1:1134062/1‑140 (MQ=255)                               aGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACt                                                                                                      <  2:897774/140‑1 (MQ=255)                                     gggCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTc                                                                                                <  1:376965/140‑1 (MQ=255)                                       gCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGAGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGc                                                                                              >  2:234514/1‑140 (MQ=255)                                           tCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGTCAcc                                                                                          >  1:945797/1‑140 (MQ=255)                                              gCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCa                                                                                       <  1:169371/140‑1 (MQ=255)                                                   ggCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGc                                                                                  <  1:264688/140‑1 (MQ=255)                                                   ggCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGc                                                                                  <  2:237386/140‑1 (MQ=255)                                                            gCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCCCCGCAACCGCCTGTTTCgg                                                                         <  2:1118088/140‑1 (MQ=255)                                                                        aTCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATc                                                             >  1:23931/1‑140 (MQ=255)                                                                             tAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCat                                                        >  2:466007/1‑140 (MQ=255)                                                                             tAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCat                                                        >  2:100289/1‑140 (MQ=255)                                                                                  tGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCTACCGCAACCGCCTGTTTCGGGTCACGGGCATCGTCATAtttt                                                   >  1:1058389/1‑140 (MQ=255)                                                                                   gCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGATTTTGTTCGCCACCGAAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTa                                                  <  2:1134062/140‑1 (MQ=255)                                                                                    ccTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTAc                                                 >  1:765984/1‑140 (MQ=255)                                                                                    ccTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTAc                                                 >  2:1085683/1‑140 (MQ=255)                                                                                    ccTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTAc                                                 >  1:620983/1‑140 (MQ=255)                                                                                     cttcgtcttcgtAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACg                                                <  1:466007/140‑1 (MQ=255)                                                                                       tcgtcttcgtAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGAt                                              >  1:518757/1‑140 (MQ=255)                                                                                                    tGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTttgttg                                 >  1:807711/1‑140 (MQ=255)                                                                                                     gTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGCTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGc                                >  2:527492/1‑140 (MQ=255)                                                                                                          aCGCAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTa                           >  1:446551/1‑140 (MQ=255)                                                                                                             cAGGCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATg                        >  1:119272/1‑140 (MQ=255)                                                                                                               ggCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATgcc                      >  1:761115/1‑140 (MQ=255)                                                                                                               ggCTGCGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATgcc                      >  2:1056590/1‑140 (MQ=255)                                                                                                                  agacaggataaAAAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGATTTTGTCCGCCCCCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATgccgcc                   <  2:1160181/134‑1 (MQ=255)                                                                                                                    cGTTGATGAAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCtt                 <  2:446551/140‑1 (MQ=255)                                                                                                                          tgaAGAACAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGt           >  2:243803/1‑140 (MQ=255)                                                                                                                          tgaAGAACAGAGGCGACCAATCACATATTTAATGCCGTCG‑TAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGtt          >  1:227798/1‑140 (MQ=255)                                                                                                                           aaagaaCAGAGGCGACCAATCAAATATTTAATCCCGTC‑TAATCGACTTTGTCCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTg         <  2:227798/139‑1 (MQ=255)                                                                                                                               aaCAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATgc                       >  1:676422/1‑123 (MQ=255)                                                                                                                               aaCAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATgc                       <  2:676422/123‑1 (MQ=255)                                                                                                                                aCAGAGGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCCCCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGatat     <  1:1085683/140‑1 (MQ=255)                                                                                                                                   gagGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGactgtct  >  1:1160181/1‑134 (MQ=255)                                                                                                                                   gagGCGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCg  >  2:1051520/1‑140 (MQ=255)                                                                                                                                       |                                                                                                                                        CCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCG  >  NC_000913/3599229‑3599498

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑