Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,255,594	Δ1 bp	coding (4/1278 nt)	yhaO ←	putative transport system permease protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,255,593	0	G	.	100.0%	414.1 / NA	90	coding (5/1278 nt)	yhaO	putative transport system permease protein
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base . (39/51);  total (39/51)

ATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGGCACGACCCGCCGGGGTCGAAGGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTC  >  NC_000913/3255518‑3255665                                                                            |                                                                         aTACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAg                                                                          >  1:4190229/1‑76 (MQ=255)   ccTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAgca                                                                        <  1:517376/75‑3 (MQ=255)   aCTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAgca                                                                        >  1:4292610/1‑74 (MQ=255)    cTCATAATCCCCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAgcac                                                                       <  1:1650776/76‑4 (MQ=255)    cTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAgcac                                                                       <  1:3309000/76‑4 (MQ=255)    cTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAgcac                                                                       <  1:3251029/76‑4 (MQ=255)    cTCATAACCCCCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAgcac                                                                       <  2:935386/76‑4 (MQ=255)      cATAACCACCCAGCCGGTGTCTGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGa                                                                    <  2:2575761/76‑1 (MQ=255)       aTAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGAc                                                                   >  1:550934/1‑76 (MQ=255)       aTAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGAc                                                                   >  2:3279656/1‑76 (MQ=255)        tAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCTCTCGCTCTCACTCATTCCA‑GCACGAcc                                                                  <  1:4186330/76‑1 (MQ=255)         aaTCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGAccc                                                                 >  2:2018472/1‑76 (MQ=255)          aTCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACccg                                                                <  1:3186377/76‑1 (MQ=255)           tCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACccgc                                                               <  2:4190229/76‑1 (MQ=255)            gccccAGCCGGTGTCGGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCGCGACccgcc                                                              <  2:2485288/74‑1 (MQ=255)            cACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACccgcc                                                              >  2:2662318/1‑76 (MQ=255)             aCCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACccgccg                                                             >  2:3866751/1‑76 (MQ=255)              cccAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCgg                                                            >  2:892570/1‑76 (MQ=255)               ccAGCGGGTTTCCGTACTGTCGAATTTGATCGCTTCTCGCCACTCTCTCTCACTCATTCCA‑GCACGCCCCGCCggg                                                           <  1:2220390/76‑1 (MQ=255)                 cgCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGt                                                         <  2:3755774/75‑1 (MQ=255)                 aGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCCTTCCA‑GCACGACCCGCCGGGGt                                                         >  2:3002849/1‑76 (MQ=255)                 aGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCggggc                                                         >  2:2619570/1‑75 (MQ=255)                 aGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGt                                                         >  2:2981102/1‑76 (MQ=255)                 aGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGt                                                         >  1:3313530/1‑76 (MQ=255)                  tccGGTGTCAATACTGGCGATTTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTc                                                        <  1:1775800/75‑1 (MQ=255)                  gCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTc                                                        >  1:3158583/1‑76 (MQ=255)                  gCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTc                                                        <  1:4218160/76‑1 (MQ=255)                  gCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTc                                                        <  1:1850650/76‑1 (MQ=255)                   ccGGGGTCAGTGCTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCg                                                       <  2:377513/76‑1 (MQ=255)                    cGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGa                                                      <  1:2102021/76‑1 (MQ=255)                    cGGTGTCAGTACTGTCGAATTTGATCGCTTCTCACCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGCCGa                                                      >  2:420214/1‑76 (MQ=255)                     ggTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGaa                                                     >  1:1744956/1‑76 (MQ=255)                      gtgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAg                                                    >  2:659928/1‑76 (MQ=255)                      gtgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAg                                                    <  2:1685709/76‑1 (MQ=255)                       tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCGCGACCCGCCGGGGTCGAAgc                                                   <  1:2096421/76‑2 (MQ=255)                       tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACccgcc                                                              >  1:658795/1‑65 (MQ=255)                       tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACccgcc                                                              <  2:658795/65‑1 (MQ=255)                       tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgc                                                   <  1:2662318/76‑2 (MQ=255)                       tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgc                                                   >  2:838871/1‑75 (MQ=255)                       tgtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgc                                                   >  2:1100482/1‑75 (MQ=255)                        gtCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgcg                                                  >  1:3554991/1‑74 (MQ=255)                         tCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAAgcgt                                                 >  2:1808816/1‑73 (MQ=255)                            gTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTg                                             <  2:3808556/76‑1 (MQ=255)                             tACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGc                                            <  1:3396071/76‑1 (MQ=255)                             gaCTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGc                                            <  2:4811565/75‑1 (MQ=255)                               cTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCaa                                          <  1:4216706/76‑1 (MQ=255)                                tGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAAt                                         <  2:532260/76‑1 (MQ=255)                                 gTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATg                                        >  1:4141840/1‑76 (MQ=255)                                 gTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATg                                        >  2:3323808/1‑76 (MQ=255)                                  tCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGa                                       <  2:2604237/76‑1 (MQ=255)                                  tCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGa                                       <  1:3322363/76‑1 (MQ=255)                                  tCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGa                                       >  1:1296636/1‑76 (MQ=255)                                   cGAATTTGATCGCTTCTCCCCCCTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGAc                                      <  2:1708721/76‑1 (MQ=255)                                    gAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACg                                     <  1:1501459/76‑1 (MQ=255)                                    gAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACg                                     >  1:2761848/1‑76 (MQ=255)                                    gAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACg                                     >  2:3646173/1‑76 (MQ=255)                                       tttGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCt                                  <  1:2098615/76‑1 (MQ=255)                                        ttGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCtt                                 <  2:3362871/76‑1 (MQ=255)                                        tggATCGCTGCTCGCCACTCGCTCGCACTCATTCCA‑GCACGACCCGCCTGGGTCGAA‑GCGTCTGCAATGACGCCtt                                 <  1:3364600/74‑1 (MQ=255)                                         tGATCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCttt                                <  1:4587099/76‑1 (MQ=255)                                           gtCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTaa                              <  2:3264854/75‑2 (MQ=255)                                            tCGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTAtt                             <  2:4243153/76‑1 (MQ=255)                                             cGCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTc                            >  2:4663674/1‑76 (MQ=255)                                              gCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCg                           >  2:3060237/1‑76 (MQ=255)                                              gCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCg                           <  1:2699187/76‑1 (MQ=255)                                              gCTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCg                           >  1:637403/1‑76 (MQ=255)                                               cTTCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGa                          >  2:3475519/1‑76 (MQ=255)                                                ttCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGAt                         <  1:1898908/76‑1 (MQ=255)                                                ttCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGAt                         >  1:121141/1‑76 (MQ=255)                                                ttCTCGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGAt                         <  1:2048822/76‑1 (MQ=255)                                                 tctcGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCgctc                        >  2:27170/1‑73 (MQ=255)                                                 tctcGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATg                        <  2:4185032/76‑1 (MQ=255)                                                  ctcGCCACTCGCACTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGc                       <  2:3470688/76‑1 (MQ=255)                                                   tcGCGACGCGCTCTCACTCATTCCA‑GCACGTCCCGCCGGGGTCGAA‑GCGGCTGCAATGACGCGTGTATGCGATGCa                      >  1:2687634/1‑76 (MQ=255)                                                    cGCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCaa                     <  2:3139512/76‑1 (MQ=255)                                                     gCCACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAt                    >  2:2168457/1‑76 (MQ=255)                                                     cccACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAt                    <  1:2428144/75‑1 (MQ=255)                                                       cACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAttt                  <  1:4396761/76‑1 (MQ=255)                                                       cACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAttt                  <  2:1744955/76‑1 (MQ=255)                                                       cACTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAAttt                  <  1:892571/76‑1 (MQ=255)                                                        ccTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTc                 <  1:690187/75‑1 (MQ=255)                                                        aCTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTc                 >  2:1382972/1‑76 (MQ=255)                                                         cTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTcc                <  1:200002/76‑1 (MQ=255)                                                         cTCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTcc                >  2:3222541/1‑76 (MQ=255)                                                          tCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCa               >  2:798592/1‑76 (MQ=255)                                                          tCGCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCa               >  2:3354575/1‑76 (MQ=255)                                                           cGCTCTCACACATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCAt              <  1:1229584/76‑1 (MQ=255)                                                           cGCTCTAACTCATTCCA‑GCACGCCCCGCCGGAGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCAt              <  1:2834731/76‑1 (MQ=255)                                                            gCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATa             >  2:4858759/1‑76 (MQ=255)                                                            gCTCTCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATa             <  1:1808817/76‑1 (MQ=255)                                                             ctctCACTCATTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATaa            >  2:4065187/1‑76 (MQ=255)                                                                 cactcaTTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATACTTtc        >  2:4748983/1‑76 (MQ=255)                                                                   ctcaTTCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTtctc      <  2:4696416/76‑1 (MQ=255)                                                                       ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc  <  2:2434982/76‑1 (MQ=255)                                                                       ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc  <  2:2462677/76‑1 (MQ=255)                                                                       ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc  <  1:3542385/76‑1 (MQ=255)                                                                       ttCCA‑GCACGACCCGCCGGGGTCGAA‑GCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTc  <  2:2497022/76‑1 (MQ=255)                                                                            |                                                                         ATACTCATAATCACCCAGCCGGTGTCAGTACTGTCGAATTTGATCGCTTCTCGCCACTCGCTCTCACTCATTCCAGGCACGACCCGCCGGGGTCGAAGGCGTCTGCAATGACGCCTTTATTCGATGCAATTTCCATAATTTCTCGCTC  >  NC_000913/3255518‑3255665

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑