Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A5 F28 I1 R1 260 73.5 2514320 99.3% 2496719 138.8

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,455,545 A→G intergenic (‑147/‑33) gspA ← / → gspC Type II secretion system protein GspA/Type II secretion system protein GspC

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,455,5450AG100.0% 225.2 / NA 63intergenic (‑147/‑33)gspA/gspCType II secretion system protein GspA/Type II secretion system protein GspC
Reads supporting (aligned to +/- strand):  ref base A (0/0);  new base G (38/25);  total (38/25)

TGATTATCCTTAATCATAAAAATAATGTATGTATTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAACCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTTATAAGCATAGGGTCGATTAT  >  NC_000913/3455420‑3455672
                                                                                                                             |                                                                                                                               
tGATTATCCTTAATCATAAAAATAATGTATGTATTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTAt                                                                                                                   >  2:1050424/1‑140 (MQ=255)
       ccTTAATCATAAAAATAATGTATGTATTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTttatta                                                                                                            <  1:765689/140‑1 (MQ=255)
           aaTCATAAAAATAATGTATGTATTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAac                                                                                                        >  2:422867/1‑140 (MQ=255)
                tAAAAATAATGTATGTATTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTtta                                                                                                               <  2:368796/128‑1 (MQ=255)
                tAAAAATAATGTATGTATTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTtta                                                                                                               >  1:368796/1‑128 (MQ=255)
                           tatgtatTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCcaca                                                                                        >  1:14733/1‑140 (MQ=255)
                                         ttaaATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCtt                                                                          >  2:109668/1‑140 (MQ=255)
                                         ttaaATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCtt                                                                          >  1:691505/1‑140 (MQ=255)
                                              tACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATc                                                                     >  1:524147/1‑140 (MQ=255)
                                                   atTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCg                                                                <  2:14733/140‑1 (MQ=255)
                                                   atTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCg                                                                >  1:1213954/1‑140 (MQ=255)
                                                   atTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCg                                                                >  2:1196897/1‑140 (MQ=255)
                                                   atTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCg                                                                >  2:431613/1‑140 (MQ=255)
                                                   atTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCg                                                                >  2:74558/1‑140 (MQ=255)
                                                     tACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGaa                                                              >  1:425390/1‑140 (MQ=255)
                                                      aCTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAAt                                                             <  2:691505/140‑1 (MQ=255)
                                                      aCTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAAt                                                             <  2:861186/140‑1 (MQ=255)
                                                      aCTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAAt                                                             >  1:285645/1‑140 (MQ=255)
                                                          ataaaaataaatTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCata                                                         >  1:217677/5‑140 (MQ=255)
                                                           tataAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCg                                                                <  2:974772/132‑1 (MQ=255)
                                                           tataAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCg                                                                >  1:974772/1‑132 (MQ=255)
                                                           tataAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCataa                                                        >  1:520249/1‑140 (MQ=255)
                                                           tataAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCataa                                                        >  2:110459/1‑140 (MQ=255)
                                                           tataAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCataa                                                        >  1:579175/1‑140 (MQ=255)
                                                           tataAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCataa                                                        >  2:1049525/1‑140 (MQ=255)
                                                           tataAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCataa                                                        >  2:689123/1‑140 (MQ=255)
                                                             taaataaaTTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCTAATCa                                                           <  2:615917/135‑1 (MQ=255)
                                                             taaataaaTTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCTAATCa                                                           >  1:615917/1‑135 (MQ=255)
                                                             taaataaaTTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCataata                                                      >  1:944315/1‑140 (MQ=255)
                                                              aaataaatTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCAtaataa                                                     <  2:285645/140‑1 (MQ=255)
                                                               aataaatTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATaaa                                                    >  1:904051/1‑140 (MQ=255)
                                                                ataaatTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAg                                                   >  1:117845/1‑140 (MQ=255)
                                                                ataaatTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAg                                                   >  2:431024/1‑140 (MQ=255)
                                                                   aatTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGAtg                                                <  1:1049525/140‑1 (MQ=255)
                                                                    atTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGaa                                                              <  1:335797/125‑1 (MQ=255)
                                                                    atTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGaa                                                              >  2:335797/1‑125 (MQ=255)
                                                                    atTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGAtgc                                               >  1:1200161/1‑140 (MQ=255)
                                                                     ttttGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGAtgct                                              <  2:425390/140‑1 (MQ=255)
                                                                     ttttGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCACACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGAtgct                                              <  1:677723/140‑1 (MQ=255)
                                                                       ttGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGAtgctgc                                            <  2:524147/140‑1 (MQ=255)
                                                                       ttGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGAtgctgc                                            <  2:904051/140‑1 (MQ=255)
                                                                       ttGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGAtgctgc                                            <  1:813655/140‑1 (MQ=255)
                                                                        tGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAAt                                                             <  1:399131/122‑1 (MQ=255)
                                                                        tGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAAt                                                             >  2:399131/1‑122 (MQ=255)
                                                                          cTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCAt                                         >  1:1222658/1‑140 (MQ=255)
                                                                                    gCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAGAGATGCTGCCATCAATATATTg                               >  1:461214/1‑140 (MQ=255)
                                                                                     cAAGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGa                              <  1:109668/140‑1 (MQ=255)
                                                                                       aGCGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGAtt                            <  1:689123/140‑1 (MQ=255)
                                                                                         cGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATtat                          >  2:1078179/1‑140 (MQ=255)
                                                                                         cGGCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATtat                          >  1:130098/1‑140 (MQ=255)
                                                                                          ggCATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAGAGATGCTGCCATCAATATATTGATtata                         <  2:461214/140‑1 (MQ=255)
                                                                                            cATTAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATAtt                       <  2:566986/140‑1 (MQ=255)
                                                                                              ttAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTta                     <  2:217677/140‑1 (MQ=255)
                                                                                               tAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTtat                    <  2:1213954/140‑1 (MQ=255)
                                                                                               tAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTtat                    <  2:1200161/140‑1 (MQ=255)
                                                                                               tAATACTATTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTtat                    <  1:74558/140‑1 (MQ=255)
                                                                                                      aTTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTtat                    >  2:65750/1‑133 (MQ=255)
                                                                                                      aTTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTtat                    <  1:65750/133‑1 (MQ=255)
                                                                                                      aTTTATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTTATAAGCATa             >  2:112933/1‑140 (MQ=255)
                                                                                                        ttATACTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTTATAAGCATAgg           >  1:1243969/1‑140 (MQ=255)
                                                                                                            aCTAACGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTTATAAGCATAGGGTCg       >  1:129301/1‑140 (MQ=255)
                                                                                                               aaCGTCAATATACAGCCCACCCAATCTATATTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCAACAATATATTGATTATATTTATAAGCATAGGGACGatt    >  2:1024270/1‑140 (MQ=255)
                                                                                                                 cGTCAATATACAGCCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCAATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTTATAAGCATAGGGTCGattat  >  2:1088487/1‑140 (MQ=255)
                                                                                                                             |                                                                                                                               
TGATTATCCTTAATCATAAAAATAATGTATGTATTTATTAATTAAATACATATTACTAATATAAATAAATTTTGCTTGATTCATGCAAGCGGCATTAATACTATTTATACTAACGTCAATATACAACCCACCCAATCTATTTTATTAGAACATACATCGTGCCCACACTACGTTTCCCCTTCCATCTGGCGAATCATAATAAAGATGCTGCCATCAATATATTGATTATATTTATAAGCATAGGGTCGATTAT  >  NC_000913/3455420‑3455672

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A