Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,599,379	T→G	K94Q (AAA→CAA)	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	3,599,379	0	T	G	100.0%	95.0 / NA	28	K94Q (AAA→CAA)	livJ	branched chain amino acid/phenylalanine ABC transporter periplasmic binding protein
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base G (22/6);  total (22/6)

ATTGCTGTTTGTCGTGAACGATAGCAATACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCACCGTACTGCGCAACCGGACCGGACATTGCGCCCACGACCGCGACTTTAATATCTTCTGCCAGAGCCATATTGCTGAATGCCAGCGCGATAC  >  NC_000913/3599142‑3599624                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                      agtGCTGTTTGTCGTGAACGATAACAATACGCTGCGGTTTTACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTa                                                                                                                                                                                                                                          <  2:26496/249‑1 (MQ=255)      tGTTTGTCGTGAACGATAGCAATACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGAc                                                                                                                                                                                                                                     >  1:382161/1‑251 (MQ=255)         ttGTCGTGAACGATAGCAATACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACttt                                                                                                                                                                                                                                  >  1:17622/1‑251 (MQ=255)           gTCGTGAACGATAGCAATACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGt                                                                                                                                                                                                                                <  1:449949/251‑1 (MQ=255)             cGTGAAAGATAGCAATCCGCTGCGGTTTAACTTTCTCAAGATTATATTTCGCCGCCGTCGGGCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACAGATTGAATGCCGTCGGTAACGACTTTGTTc                                                                                                                                                                                                                              <  1:134566/251‑1 (MQ=255)               ggAACGATAGCAATACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGc                                                                                                                                                                                                                            <  1:89091/250‑1 (MQ=255)                  accatggcaactcGCTGCGGTGTCCTTTTCACAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCTCGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCGTCGTAGATGTCAGACGCAGGCTGCGTTGATTAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCAc                                                                                                                                                                                                                         <  1:61587/239‑1 (MQ=255)                   cGATAGCAATACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGACCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCAcc                                                                                                                                                                                                                        >  1:275105/1‑251 (MQ=255)                           aTACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCATGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGc                                                                                                                                                                                                                >  1:289611/1‑251 (MQ=255)                                    ggattCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGGGATCATTAAAATGCCTTCGTCTTCGGAGATGTCAGACGCAGGCAGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGATAACGACTTTGTTCGCCACCGCAACCACCTGTTTCgg                                                                                                                                                                                                       >  2:367538/4‑251 (MQ=255)                                                tcAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATc                                                                                                                                                                                           >  1:205388/1‑251 (MQ=255)                                                               gccgccGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCGTCGTCATCTTTTACGAt                                                                                                                                                                            >  1:396284/1‑251 (MQ=255)                                                               gccgccGTCGGCCCCTGGTCGGAGTCCAGGCCGGCGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCGGTTTCGGGTCACAGGCATCGACATATTTTACg                                                                                                                                                                              >  1:175085/1‑249 (MQ=255)                                                                       cGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGACACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGtt                                                                                                                                                                    >  1:358501/1‑251 (MQ=255)                                                                                 ggggAGTCCGGGGCGGGGGTGCGCAGGATCAGCGGATACCCAGGGGCGTACAGCTCCGGCGCGGTTGCCGGTGGGGTGACCATAAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGGTGATGAAGAACAGAGGTGACCAATCACATATGGAATGCCGTCGTTAACGTTTTTTTCCCCCACCGCAACCGCCTGGTTCGGGTCACAGGCATCGTCATATTTTACGATTTGGAGTTTGTTGCCttt                                                                                                                                                          <  1:364008/249‑1 (MQ=255)                                                                                    gAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCATCGTTAACGACTTTGGTCGCCACCGCAACCGCCTGTTTCGGGTCACCGGCATCGACATATTTTACGATTTGCAGTTTGTTGCCGTTAAt                                                                                                                                                       >  1:301003/1‑251 (MQ=255)                                                                                                                  tGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGc                                                                                                                         >  1:148080/1‑251 (MQ=255)                                                                                                                   gATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGcc                                                                                                                        >  1:76533/1‑251 (MQ=255)                                                                                                                                                          gggTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGATCACCGTACTgcgc                                                                                  >  1:312996/1‑250 (MQ=255)                                                                                                                                                           ggTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTTACGTCTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCAACGTACTGCGCa                                                                                 >  1:175509/1‑250 (MQ=255)                                                                                                                                                             tGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCACCGTACTGCGCAacc                                                                              >  1:228476/1‑251 (MQ=255)                                                                                                                                                                       aaTGCCTTCTTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGTTTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATACGCAACCGCCTGCTCTGCTCCGTTATACTCCTGGTCACAGTTCTGCGCAACcggcccggact                                                                    >  2:139894/1‑250 (MQ=255)                                                                                                                                                                           ccTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGCTGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTACCGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTAACAGGCATCGTCATATTTTACGCTTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTACTATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCGGGTCACCGAACTGCGCAACCGGACCGGACATTgg                                                                >  2:414643/1‑250 (MQ=255)                                                                                                                                                                               cgtcttcgtAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCACCGTACTGCGCAACCGGACCGGACATTGCGccc                                                            >  1:116979/1‑251 (MQ=255)                                                                                                                                                                                                     aGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTGAATGCCGTCGTTTACGCCTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCCTCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCCCCGTACTGCGCAACCGGACCGGACATAGCGCCCACGACCGCGACTTTAATAtctt                                      >  1:352424/1‑251 (MQ=255)                                                                                                                                                                                                            gTTGATGAAGAACAGAGGTGACCAATCACATATTGTATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCACCGTACTGCGCAACCGGACCGGACATTGCGCCCACGACCGCGACTTTAATATCTTCTGcc                                 >  1:368540/1‑249 (MQ=255)                                                                                                                                                                                                                                         atatTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCACCGTACTGCGCAACCGGACCGGACATTGCGCCCACGACCGCGACTTTAATATCTTCTGCCAGAGCCATATTGCTGAATGCCAGCGCGATAc  >  1:418170/1‑251 (MQ=255)                                                                                                                                                                                                                                          tatTGAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCACCGTACTGCGCAACCGGACCGGCCATTGCGCCCACGACCGCGACTTTAATATCTTCTGCCAGAGCCATATTGCTGAATGCCAGCGCGATAc  >  2:266730/1‑250 (MQ=255)                                                                                                                                                                                                                                              |                                                                                                                                                                                                                                                      ATTGCTGTTTGTCGTGAACGATAGCAATACGCTGCGGTTTCACTTTCTCAAGAATATATTTCGCCGCCGTCGGCCCCTGGTCGGAGTCCAGGCCGGTGGTGCGCAGGATCAGCTGATAGCCACGGGCGGTCAGCTCCGGCGCGGTTGCCGCTGGGGTGATCATTAAAATGCCTTCGTCTTCGTAGATGTCAGACGCAGGCTGCGTTGATGAAGAACAGAGGTGACCAATCACATATTTAATGCCGTCGTTAACGACTTTGTTCGCCACCGCAACCGCCTGTTTCGGGTCACAGGCATCGTCATATTTTACGATTTGCAGTTTGTTGCCTTTAATGCCGCCTTTAGCGTTGATATCCGCAACCGCCTGCTCTGCGCCGGTAAACTCCTGGTCACCGTACTGCGCAACCGGACCGGACATTGCGCCCACGACCGCGACTTTAATATCTTCTGCCAGAGCCATATTGCTGAATGCCAGCGCGATAC  >  NC_000913/3599142‑3599624

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑