Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,082,796	G→A	intergenic (+125/+81)	loiP → / ← speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein/agmatinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,082,796	0	G	A	100.0%	189.8 / NA	59	intergenic (+125/+81)	loiP/speB	Phe‑Phe periplasmic metalloprotease, OM lipoprotein, low salt‑inducible, Era‑binding heat shock protein/agmatinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (35/24);  total (35/24)

GGGATTAAGTAAAGCCTGGTGGTGTCGAACGTAGGTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTCCAGCGCCAGCGTTGCC  >  NC_000913/3082660‑3082931                                                                                                                                         |                                                                                                                                        gggATTAAGAAAAGCCTTGTGGTGTCGAACGTAGGTCAGATAAGGCGTTCAAGCCGCCTCTGACATGAATGGCACATTTTTTTCCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTTACCGGCCTACGGGTAcc                                                                                                                                       <  1:989279/139‑1 (MQ=38)        aGTAAAGCCTGGTGGTGTCGAACGTAGGTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTAT‑CGGCCTACGGGTACCGAACGTAg                                                                                                                               <  2:948982/139‑1 (MQ=255)               cccggtggtGTCGAACGTAGGTCAGATACGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATCCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGa                                                                                                                         >  1:882728/4‑139 (MQ=255)                   gtggtgTCGAACGTAGGTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAg                                                                                                                     >  1:1006058/1‑139 (MQ=255)                            aaCGTAGGTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcg                                                                                                            >  1:461592/1‑139 (MQ=255)                             aCGTAGGTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcgc                                                                                                           <  2:1006058/139‑1 (MQ=255)                                  ggTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCAt                                                                                                      >  2:1578275/1‑139 (MQ=255)                                   gTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGt                                                                                                                             <  2:681890/115‑1 (MQ=255)                                   gTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGt                                                                                                                             >  1:681890/1‑115 (MQ=255)                                             gCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcgccg                                                                                                         >  1:1060758/1‑125 (MQ=255)                                             gCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcgccg                                                                                                         <  2:1060758/125‑1 (MQ=255)                                               gTTTACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                                                                                         <  2:1037497/139‑1 (MQ=255)                                                                 aTGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcg                                                                                                            <  2:919975/102‑1 (MQ=255)                                                                 aTGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcg                                                                                                            >  1:919975/1‑102 (MQ=255)                                                                         cacaTTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCgcatcgcatc                                                               <  1:1163575/139‑1 (MQ=255)                                                                         cacaTTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCgcatcgcatc                                                               <  2:461592/139‑1 (MQ=255)                                                                              ttGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTg                                                          >  2:313744/1‑139 (MQ=255)                                                                                    ccTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACt                                                    <  2:882728/139‑1 (MQ=255)                                                                                      ttGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgca                                                                      <  2:1540862/119‑1 (MQ=255)                                                                                      ttGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgca                                                                      >  1:1540862/1‑119 (MQ=255)                                                                                      ttGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCg                                                  >  2:217798/1‑139 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                                                                                         >  1:1306534/1‑98 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                                                                                         <  2:1306534/98‑1 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatcgcat                                                                >  1:1132215/1‑123 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatcgcat                                                                <  2:451191/123‑1 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatcgcat                                                                >  1:451191/1‑123 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatcgcat                                                                <  2:1132215/123‑1 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGcc                                                >  1:704522/1‑139 (MQ=255)                                                                                        gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGcc                                                >  2:1335535/1‑139 (MQ=255)                                                                                         tgcacATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAc                                                                                                 <  2:487121/85‑1 (MQ=255)                                                                                         tgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGccc                                               >  1:1470085/1‑139 (MQ=255)                                                                                         tgCACATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGAc                                                                                                 >  1:487121/1‑89 (MQ=255)                                                                                              aTTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCttttt                                          >  2:1477722/1‑139 (MQ=255)                                                                                                tGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACAGGTACTGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTcg                                        >  2:1076790/1‑139 (MQ=255)                                                                                                   cGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTcgccg                                     >  2:322552/1‑139 (MQ=255)                                                                                                       acagatgcTGGCCCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGGCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCCTTTTCGCCGCCTg                                 <  2:383333/136‑1 (MQ=39)                                                                                                        gcgatgcTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGa                                <  1:1477722/139‑1 (MQ=255)                                                                                                          gatgcTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCTTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGa                                <  1:1294086/137‑1 (MQ=255)                                                                                                          gatgcTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGa                                >  2:1294086/1‑137 (MQ=255)                                                                                                            tgcTGGCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAatat                            >  2:553788/1‑139 (MQ=255)                                                                                                                ggCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                                                                                         <  2:752968/74‑1 (MQ=255)                                                                                                                ggCGCATCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                                                                                         >  1:752968/1‑74 (MQ=255)                                                                                                                     aTCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCAttt                   >  2:978243/1‑139 (MQ=255)                                                                                                                      tCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                                                                                         <  2:1415580/68‑1 (MQ=255)                                                                                                                      tCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                                                                                         >  1:1415580/1‑68 (MQ=255)                                                                                                                      tCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTc                  >  1:91393/1‑139 (MQ=255)                                                                                                                      tCTTATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCCCCCCTTTTCCCCCCCTAATTATCCacaattgt                  >  1:383333/1‑132 (MQ=37)                                                                                                                        ttATCCGGCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTcca                >  2:273979/1‑139 (MQ=255)                                                                                                                               gCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTg                                                                          <  2:1557727/74‑1 (MQ=255)                                                                                                                               gCCTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTg                                                                          >  1:1557727/1‑74 (MQ=255)                                                                                                                                ccTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTccagcgccagc        >  2:477922/1‑139 (MQ=255)                                                                                                                                ccTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTccagcgccagc        >  1:886796/1‑139 (MQ=255)                                                                                                                                 cTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTccagcgccagcg       >  1:333765/1‑139 (MQ=255)                                                                                                                                 cTACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTccagcgccagcg       <  1:273979/139‑1 (MQ=255)                                                                                                                                  tACGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACACGTGCGCATCGCCTCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTCCAGCGCCAGCGt      >  1:257954/1‑139 (MQ=255)                                                                                                                                    cGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcgc                                                                                                           <  2:164295/36‑1 (MQ=17)                                                                                                                                    cGGGTACCGAACGTAGGTCGGATAAGGCGTTCAcgc                                                                                                           >  1:164295/1‑36 (MQ=17)                                                                                                                                    cGGGTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTCCAGCGCCAGCGTTg    >  1:463568/1‑139 (MQ=255)                                                                                                                                      ggTACCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTCCAGCGCCAGCGTTGcc  <  1:1335535/139‑1 (MQ=255)                                                                                                                                         |                                                                                                                                        GGGATTAAGTAAAGCCTGGTGGTGTCGAACGTAGGTCAGATAAGGCGTTCACGCCGCATCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATCGCATCTGGTGCTTACTCGCCCTTTTTCGCCGCCTGAATATACAGCATTTCCAGCGCCAGCGTTGCC  >  NC_000913/3082660‑3082931

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑