Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,853,909	A→G	intergenic (+267/‑13)	tisB → / → emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,853,909	0	A	G	100.0%	225.5 / NA	62	intergenic (+267/‑13)	tisB/emrD	toxic membrane persister formation peptide, LexA‑regulated/multidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (37/25);  total (37/25)

CCTGGCGTATATCTGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTA  >  NC_000913/3853814‑3854001                                                                                                |                                                                                             ccTGGCGTATATCTGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCAt                                                                                          >  2:1309959/1‑100 (MQ=255)   tGGCGTATATCTGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATcc                                                                                        <  1:866480/100‑1 (MQ=255)      cGTATATCTGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTg                                                                                     <  1:85396/100‑1 (MQ=255)       gTATATCTGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGa                                                                                    <  1:85742/100‑1 (MQ=255)            tCTAGCTAACATTCATCAATGAGATAGATTCCTCTCCCACATTTATAGGAATGCGTAGTGACTTATTATAATCATTTATATAAAGGCATCCGTGATAATg                                                                               <  2:703962/100‑1 (MQ=255)             cTGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGa                                                                              >  1:616196/1‑100 (MQ=255)              tGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGaa                                                                             <  2:408028/100‑1 (MQ=255)               ggCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGaaa                                                                            >  1:1543887/1‑100 (MQ=255)                gCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGaaaa                                                                           <  1:865315/100‑1 (MQ=255)                   aaCATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGc                                                                        >  1:1127337/1‑100 (MQ=255)                   aaCATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGc                                                                        <  1:2999/100‑1 (MQ=255)                        tcatcaATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGa                                                                   >  2:1136481/1‑100 (MQ=255)                        tcatcaATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGa                                                                   >  1:194097/1‑100 (MQ=255)                         catcaATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGaa                                                                  >  2:1346643/1‑100 (MQ=255)                           tcaATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAAc                                                                >  1:1231323/1‑100 (MQ=255)                            caATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACg                                                               <  2:443231/100‑1 (MQ=255)                              aTGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTc                                                             <  2:1012281/100‑1 (MQ=255)                                gtgATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCaa                                                           >  2:1136972/1‑100 (MQ=255)                                    tAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTg                                                       <  1:1053343/100‑1 (MQ=255)                                     aGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGt                                                      >  1:920321/1‑100 (MQ=255)                                      gATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGtt                                                     >  1:217004/1‑100 (MQ=255)                                      gATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGtt                                                     >  1:677835/1‑100 (MQ=255)                                        ttCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTAt                                                   <  1:833015/100‑1 (MQ=255)                                         tCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTAtt                                                  <  1:13091/100‑1 (MQ=255)                                          ccTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTg                                                 >  2:1221854/1‑100 (MQ=255)                                           ctctCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGa                                                >  2:762285/1‑100 (MQ=255)                                           ctctCCCGCATTTATGGGAATGCGTAATGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGa                                                >  1:958104/1‑100 (MQ=255)                                               cccGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGtt                                            >  1:336613/1‑100 (MQ=255)                                               cccGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGtt                                            >  1:1118882/1‑100 (MQ=255)                                               cccGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGtt                                            >  2:109534/1‑100 (MQ=255)                                               cccGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGtt                                            >  1:1073290/1‑100 (MQ=255)                                                ccGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTg                                           >  1:889754/1‑100 (MQ=255)                                                 cGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTgg                                          <  2:653470/100‑1 (MQ=255)                                                 cGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTgg                                          <  2:677832/100‑1 (MQ=255)                                                 cGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTgg                                          <  1:1412575/100‑1 (MQ=255)                                                    aTTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTAt                                       <  2:889746/100‑1 (MQ=255)                                                    aTTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTAt                                       >  2:1241238/1‑100 (MQ=255)                                                       tATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTAc                                    <  1:1017247/100‑1 (MQ=255)                                                          gggAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCg                                 >  2:953689/1‑100 (MQ=255)                                                           ggAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGt                                >  2:385525/1‑100 (MQ=255)                                                            gAATGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTg                               <  2:194096/100‑1 (MQ=255)                                                              aTGCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGc                             <  1:1309968/100‑1 (MQ=255)                                                                gCGTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCg                           >  2:1509835/1‑100 (MQ=255)                                                                  gTAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTc                         <  1:1482898/100‑1 (MQ=255)                                                                   tAGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTAATGAGGTTGTTATTACTCGTGGCCGTCg                        >  1:1068799/1‑100 (MQ=255)                                                                    aGTGACTTATTCTAATTATTTTTATAAAGGCATCGGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCgg                       >  2:400252/1‑100 (MQ=255)                                                                    aGTGACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCgg                       <  1:844602/100‑1 (MQ=255)                                                                       gACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCa                    >  2:413100/1‑100 (MQ=255)                                                                       gACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCa                    >  1:629787/1‑100 (MQ=255)                                                                       gACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAAATTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCa                    >  1:1415519/1‑100 (MQ=255)                                                                       gACTTATTCTAATTATTTTTATAAAGGCATCCGTGATAAGGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCa                    <  1:1259682/100‑1 (MQ=255)                                                                          ttATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGAt                 >  1:163771/1‑100 (MQ=255)                                                                           tATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATg                >  2:772113/1‑100 (MQ=255)                                                                           tATTCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATg                >  2:1073331/1‑100 (MQ=255)                                                                              tCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGgcg             >  2:1142847/1‑100 (MQ=255)                                                                              tCTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGgcg             <  1:953697/100‑1 (MQ=255)                                                                               ntAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGgcg             >  2:171642/2‑99 (MQ=255)                                                                               cTAATTATTTTTATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGgcg             >  2:684348/1‑99 (MQ=255)                                                                                      tttttATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGTTCAGATGGCGCAAACCAt     >  1:191794/1‑100 (MQ=255)                                                                                        tttATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCAttt   <  2:1264417/100‑1 (MQ=255)                                                                                        nttATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCAttt   >  2:549769/2‑100 (MQ=255)                                                                                         ttATAAAGGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTta  <  2:891315/100‑1 (MQ=255)                                                                                                |                                                                                             CCTGGCGTATATCTGGCTAACATTCATCAATGTGATAGATTCCTCTCCCGCATTTATGGGAATGCGTAGTGACTTATTCTAATTATTTTTATAAAAGCATCCGTGATAATGAAAAGGCAAAGAAACGTCAATTTGTTATTGATGTTGGTATTACTCGTGGCCGTCGGTCAGATGGCGCAAACCATTTA  >  NC_000913/3853814‑3854001

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑