Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,082,793	G→A	intergenic (+122/+84)	loiP → / ← speB	metalloprotease LoiP/agmatinase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,082,793	0	G	A	100.0%	178.7 / NA	48	intergenic (+122/+84)	loiP/speB	metalloprotease LoiP/agmatinase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (20/28);  total (20/28)

TCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATC  >  NC_000913/3082718‑3082865                                                                            |                                                                         tCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGcc                                                                     >  1:574704/1‑81 (MQ=255)     aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGcc                                                                     <  1:574632/77‑1 (MQ=255)     aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGcc                                                                     <  2:574636/77‑1 (MQ=255)     aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCg                                                                    <  1:574635/78‑1 (MQ=255)     aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGaa                                                                  <  2:574634/80‑1 (MQ=255)     aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGaa                                                                  <  1:574631/80‑1 (MQ=255)     aCATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGaa                                                                  <  1:574633/80‑1 (MQ=255)           aTGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGt                                                           <  1:574637/81‑1 (MQ=255)              gCACATTTGTTACCTTGTGCGCATTGGCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCgg                                                        <  1:574639/81‑1 (MQ=255)              gCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCgg                                                        <  2:574638/81‑1 (MQ=255)              gCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCgg                                                        <  2:574640/81‑1 (MQ=255)                 caTTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATa                                                     <  1:574641/81‑1 (MQ=255)                  aTTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATaa                                                    <  2:574642/81‑1 (MQ=255)                     tGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGc                                                 >  1:574739/1‑81 (MQ=255)                      gTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGc                                                 <  2:574643/80‑1 (MQ=255)                       ttACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCg                                                <  1:574645/80‑1 (MQ=255)                       ttACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGt                                               <  1:574644/81‑1 (MQ=255)                       ttACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGt                                               <  1:574646/81‑1 (MQ=255)                         aCCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGtt                                              <  2:574647/80‑1 (MQ=255)                         aCCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGtt                                              >  2:574711/1‑80 (MQ=255)                           cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           <  2:574649/81‑1 (MQ=255)                           cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           >  1:574731/1‑81 (MQ=255)                           cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           <  1:574650/81‑1 (MQ=255)                           cTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAc                                           <  1:574648/81‑1 (MQ=255)                              gtgCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCAcgcc                                        >  2:574719/1‑81 (MQ=255)                                   cATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATc                                   <  1:574651/81‑1 (MQ=255)                                    aTTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATcc                                  >  2:574740/1‑81 (MQ=255)                                      tGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGa                                >  1:574720/1‑81 (MQ=255)                                       gCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGa                                >  1:574718/1‑80 (MQ=255)                                         cGGATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAt                             >  2:574730/1‑81 (MQ=255)                                          ggATGCGATGCTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAt                             >  1:574723/1‑80 (MQ=255)                                           gatgcgatgcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACAtt                            >  1:574714/1‑80 (MQ=255)                                               cgatgcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATgg                       >  1:574717/1‑81 (MQ=255)                                                   gcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACg                   >  1:574756/1‑81 (MQ=255)                                                   gcTGGCGCATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACg                   >  2:574736/1‑81 (MQ=255)                                                       gcgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGtttt               <  1:574654/81‑1 (MQ=255)                                                       gcgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGtttt               <  2:574653/81‑1 (MQ=255)                                                       gcgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGtt                 <  1:574652/79‑1 (MQ=255)                                                        cgcATCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTa              <  1:574655/81‑1 (MQ=255)                                                            tCTTATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCg          >  2:574745/1‑81 (MQ=255)                                                              ttATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTg        >  2:574724/1‑81 (MQ=255)                                                               tATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTgc       >  2:574725/1‑81 (MQ=255)                                                               tATCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTgc       >  1:574738/1‑81 (MQ=255)                                                                aTCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGt         <  1:574657/78‑1 (MQ=255)                                                                aTCCGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTg        <  1:574656/79‑1 (MQ=255)                                                                   cGGCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcat   >  2:574722/1‑81 (MQ=255)                                                                    ggCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatc  <  1:574658/81‑1 (MQ=255)                                                                    ggCCTACGAGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGcgcatc  >  1:574766/1‑81 (MQ=255)                                                                            |                                                                         TCTGACATGAATGGCACATTTGTTACCTTGTGCGCATTGCCGGATGCGATGCTGGCGCATCTTATCCGGCCTACGGGTGCCGAACGTAGGTCGGATAAGGCGTTCACGCCGCATCCGACATTAATGGCACGTTTTACCCGTGCGCATC  >  NC_000913/3082718‑3082865

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑