Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	AM260479	724,768	+C	coding (82/669 nt)	lysE →	lysine efflux permease

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	AM260479	724,766	1	.	C	100.0%	78.1 / NA	21	R27P (CGC→CCC)	lysE	lysine efflux permease
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (9/12);  total (9/12)

CGTGATCCTGGGTGTAGTGGCGTGAGGTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCG‑CCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCATGTGTTCTGGGTCTGCCTGGTGTGCGCGCTTTCC  >  AM260479/724636‑724890                                                                                                                                    |                                                                                                                             cGTGATCCTGGGTGTAGTGGCGTGAGGTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACgccg‑ccc                                                                                                                           >  1:174331/1‑133 (MQ=255)         tGGGTGTAGTGGCGTGAGGTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGc                                                                                                                    >  1:635443/1‑134 (MQ=255)             tgtAGTGGCGTGAGGTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTtct                                                                                                                <  2:529917/134‑1 (MQ=255)                         aGGTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCttt                                                                                                    <  2:635443/134‑1 (MQ=255)                           gTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTcc                                                                                                  >  2:912318/1‑134 (MQ=255)                           gTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTcc                                                                                                  >  2:446782/1‑134 (MQ=255)                                        aGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCAcgccggg                                                                                                                             >  1:292852/1‑92 (MQ=255)                                        aGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCAcgccggg                                                                                                                             <  2:292852/94‑3 (MQ=255)                                         ggAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCAt                                                                                    <  1:617394/134‑1 (MQ=255)                                                                            cGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGt                                                 <  1:912318/134‑1 (MQ=255)                                                                                    aataatAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTg                                                                                        <  1:460488/87‑1 (MQ=255)                                                                                    aataatAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTg                                                                                        >  2:460488/1‑87 (MQ=255)                                                                                            ccACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCAtgt                                 >  2:970841/1‑134 (MQ=255)                                                                                                ccAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCATGTGTTc                             <  2:174331/134‑1 (MQ=255)                                                                                                ccAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCATGTGTTc                             <  2:345777/134‑1 (MQ=255)                                                                                                ccAAAAAAACAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCATGTGTTc                             <  1:970841/134‑1 (MQ=255)                                                                                                  aaaaaaaCAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCg                                                                                                          >  1:992579/1‑55 (MQ=255)                                                                                                  aaaaaaaCAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCg                                                                                                          <  2:992579/55‑1 (MQ=255)                                                                                                  aaaaaaaCAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGa                                       >  2:509301/1‑122 (MQ=255)                                                                                                  aaaaaaaCAGCCGTTCCACATCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGa                                       <  1:509301/122‑1 (MQ=255)                                                                                                                   acaTCCAATGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCATGTGTTCTGGGTCTGCCTGGTGTgcg          >  2:188440/1‑134 (MQ=255)                                                                                                                           tGCACGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCATGTGTTCTGGGTCTGCCTGGTGTGCGCGCTTTcc  <  1:188440/134‑1 (MQ=255)                                                                                                                              aCGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCAtg                                  >  2:488579/1‑99 (MQ=255)                                                                                                                              aCGCCGCCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCAtg                                  <  1:488579/99‑1 (MQ=255)                                                                                                                               cgccgcCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTg                                                                                        >  1:70552/1‑44 (MQ=38)                                                                                                                               cgccgcCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTg                                                                                        <  2:70552/44‑1 (MQ=38)                                                                                                                               cgccgcCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCAt                                                                                    >  2:179964/1‑48 (MQ=39)                                                                                                                               cgccgcCCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCAt                                                                                    <  1:179964/48‑1 (MQ=39)                                                                                                                                    |                                                                                                                             CGTGATCCTGGGTGTAGTGGCGTGAGGTAGTCCTGCGGCAGGAATGGGAAGATGGGCGGGCATGGCGGCTGCCCCCGGCGTGCAATAATAGCCACCCAAAAAAACAGCCGTTCCACATCCAATGCACGCCG‑CCTGGCCGGCTTCTCCCTCGGTCTTTCCCTGATTCTTGCCATCGGTTCCCAGAATGCTTTCGTGCTGCGACAAGGGTTGCGGCGCGAGCATGTGTTCTGGGTCTGCCTGGTGTGCGCGCTTTCC  >  AM260479/724636‑724890

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑