Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,111,797	G→A	pseudogene (192/861 nt)	yghE ←	putative type II secretion system L‑type protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,111,797	0	G	A	100.0%	101.0 / NA	32	pseudogene (192/861 nt)	yghE	putative type II secretion system L‑type protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (21/11);  total (21/11)

GGCAGAGCTGTAACGGTCAGGCGTTCAGCGTCTGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGGAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGGCGCGACGGTAGCGCGGG  >  NC_000913/3111678‑3111930                                                                                                                        |                                                                                                                                      ggCAGAGCTGTAACGGGCAGGCGGTCAGCGTCTGCGCCAGCCCCCGCTGATAGCTTTTTCGGGGCAATGCCGACCACGGGTAGCGGAAGCGGGAAATCCTGCTCATTTAGCTGGGCGCGGAACAAGACCGGAgccagcgc                                                                                                                   >  2:402106/1‑140 (MQ=255)         tGTAACGGTCAGGCGTTCAGCGTCTGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCgg                                                                                                           <  1:402106/140‑1 (MQ=255)                gTCAGGCGTTCAGCGTCTGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCa                                                                                                    >  2:435280/1‑140 (MQ=255)                   aGGCGTTCAGCGTCTGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGATACATGACAGGAACCTGCGCCAGCCCGGCGCTCCATcc                                                                                                 >  1:176225/1‑140 (MQ=255)                    ggCGTTCAGCGTCTGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGTGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATccc                                                                                                <  1:334042/140‑1 (MQ=255)                                 tGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTcc                                                                                                     >  1:76747/1‑122 (MQ=255)                                 tGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTcc                                                                                                     <  2:76747/122‑1 (MQ=255)                                                  aTAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGt                                                                  >  2:583024/1‑140 (MQ=255)                                                       ttttCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTgcgc                                                             >  2:414620/1‑140 (MQ=255)                                                         ttCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCAt                                                           >  2:107253/1‑140 (MQ=255)                                                          tCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATc                                                          >  2:110842/1‑140 (MQ=255)                                                            cGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGc                                                        >  1:564666/1‑140 (MQ=255)                                                             ggTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCa                                                       <  1:617287/140‑1 (MQ=255)                                                               tGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAg                                                     <  1:647587/140‑1 (MQ=255)                                                                      ccGACTACGGTTAGCGACAGCGTTAAATCCTGCTCATTGTGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATaaa                                              <  2:240605/140‑1 (MQ=255)                                                                           tACGGTTAGCGAAAGCGTTAAACCCTGCTCATTGATCTGCGCGCGAAATATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCcac                                         <  2:242946/140‑1 (MQ=255)                                                                            aCGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCcaca                                        <  1:154234/140‑1 (MQ=255)                                                                                ttAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGGATTGCAAGCCATAAACCCACAAGGa                                    >  1:242946/1‑140 (MQ=255)                                                                                  aGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGTCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAAt                                  >  1:526604/1‑140 (MQ=255)                                                                                   gCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATg                                 >  2:10680/1‑140 (MQ=255)                                                                                   gCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATg                                 >  1:643952/1‑140 (MQ=255)                                                                                    cGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATgg                                <  1:10680/140‑1 (MQ=255)                                                                                          cGGTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATcc                          >  1:114326/1‑140 (MQ=255)                                                                                            gTAAATCCTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAg                        >  2:557659/1‑140 (MQ=255)                                                                                                  ccTGCTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGgc                  >  2:14249/1‑140 (MQ=255)                                                                                                   cTGCTCATTGAGCTGGGCGCGAAACATTACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGgcg                 <  2:602758/140‑1 (MQ=255)                                                                                                      cTCATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCCCATCGCAAGCCACAAATGCACAAGGAATGGTCATCCAGTGCGGCGCGa              >  2:315274/1‑140 (MQ=255)                                                                                                        cATTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGGCGCGACg            <  1:110842/140‑1 (MQ=255)                                                                                                         aTTGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGGCGCGACgg           >  2:135919/1‑140 (MQ=255)                                                                                                           tGAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGGCGCGACGGTa         >  2:575171/1‑140 (MQ=255)                                                                                                           cgAGCTGGGCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGGCGCGACGGTa         >  1:607109/2‑140 (MQ=255)                                                                                                                  ggCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAGGGAATGGTCATGCAATCCGGCGCGACGGTAGCGCggg  >  1:169161/1‑140 (MQ=255)                                                                                                                  ggCGCGAAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGGCATCCAGTCCGGCGCGACGGTAGCGCggg  >  1:46774/1‑140 (MQ=255)                                                                                                                        |                                                                                                                                      GGCAGAGCTGTAACGGTCAGGCGTTCAGCGTCTGCGCCAGCCCATGCTGATAGCTTTTCCGGTGCAATGCCGACTACGGTTAGCGAAAGCGGTAAATCCTGCTCATTGAGCTGGGCGCGGAACATGACCGGAGCCAGCGCCAGCCCGGCGCTCCATCCCCGGCATTCATCGATGCGGCAGATAACCCGTTGCGCATCGCAAGCCATAAACCCACAAGGAATGGACATCCAGTCCGGCGCGACGGTAGCGCGGG  >  NC_000913/3111678‑3111930

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑