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
A12 F133 I1 R1 102 83.9 4092546 96.1% 3932936 99.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 3,582,272 G→A C137Y (TGT→TAT)  yhhZ → putative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009133,582,2720GA98.8% 289.7 / ‑4.5 83C137Y (TGT→TAT) yhhZputative Hcp1 family polymorphic toxin protein; putative colicin‑like DNase/tRNase activity
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (39/42);  total (40/43)
Fisher's exact test for biased strand distribution p-value = 4.88e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

CAACTAAGAGGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTGTCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACCAAACAAATAA  >  NC_000913/3582175‑3582368
                                                                                                 |                                                                                                
cAACTAAGAGGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATc                                                                                                <  2:1817464/100‑1 (MQ=255)
cAACTAAGAGGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATc                                                                                                >  1:1409274/1‑100 (MQ=255)
   cTAAGAGGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAAc                                                                                             >  2:1391228/1‑100 (MQ=255)
     aaGAGGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACAt                                                                                           >  1:1645801/1‑100 (MQ=255)
     aaGAGGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTATATCaa                                                                                              >  2:1631677/1‑97 (MQ=255)
       gagGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCt                                                                                         <  1:293026/100‑1 (MQ=255)
           cgcTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATc                                                                                     >  2:1447026/1‑100 (MQ=255)
            gcTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATcn                                                                                    <  2:1409265/100‑2 (MQ=255)
             cTTTTTTATCGGCTATTCATCACCAGATCATTGAAATCCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGc                                                                                   <  1:1944657/100‑1 (MQ=255)
              ttttttATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCa                                                                                  >  2:481253/1‑100 (MQ=255)
               tttttATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCaa                                                                                 >  1:49047/1‑100 (MQ=255)
                 tttATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAAt                                                                               <  1:1160865/100‑1 (MQ=255)
                 tttATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAAt                                                                               <  1:387052/100‑1 (MQ=255)
                  ttATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATa                                                                              <  1:1981142/100‑1 (MQ=255)
                     tCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCg                                                                           <  2:1355113/100‑1 (MQ=255)
                      cGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGa                                                                          <  1:1270031/100‑1 (MQ=255)
                       ggCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAg                                                                         >  1:816962/1‑100 (MQ=255)
                       ggCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAg                                                                         >  2:727330/1‑100 (MQ=255)
                       ggCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAg                                                                         <  2:216103/100‑1 (MQ=255)
                        gCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGt                                                                        <  1:1450413/100‑1 (MQ=255)
                          tATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTc                                                                      >  2:563582/1‑100 (MQ=255)
                          gatctatcaCCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTc                                                                      <  2:1999754/95‑1 (MQ=255)
                           aTTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCa                                                                     <  2:2011294/100‑1 (MQ=255)
                               atcaCCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAgatc                                                                 >  1:1999772/1‑97 (MQ=255)
                                     aGATCATTGAAAACCAACTGGATACAGAAACAATGACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGc                                                           <  1:1607424/100‑1 (MQ=255)
                                     aGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGc                                                           <  1:1666562/100‑1 (MQ=255)
                                     aGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGc                                                           <  1:1391237/100‑1 (MQ=255)
                                     aGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGc                                                           <  1:1387326/100‑1 (MQ=255)
                                     aGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGc                                                           <  2:1529480/100‑1 (MQ=255)
                                      gATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCa                                                          >  2:1025696/1‑100 (MQ=255)
                                       aTCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCAc                                                         <  1:1485051/100‑1 (MQ=255)
                                          aTTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTcc                                                      >  1:1876274/1‑100 (MQ=255)
                                          aTTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTcc                                                      <  1:2033903/100‑1 (MQ=255)
                                          aTTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTc                                                       >  2:331974/1‑99 (MQ=255)
                                           ttGAAAACCTACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTccc                                                     >  2:1603605/1‑100 (MQ=255)
                                           ttGAAAACCAACTGGATACAGAAACAATAACAATTAGTTATGAATTTATCCCCTATCAAAATCTTATCGCAAATAACGAGTTCAGCTATTTGGCACTccc                                                     >  2:1037274/1‑100 (MQ=255)
                                            tGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCt                                                    >  2:1112639/1‑100 (MQ=255)
                                             gAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTg                                                   >  1:601476/1‑100 (MQ=255)
                                             gAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTg                                                   <  1:1101201/100‑1 (MQ=255)
                                                aaCCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGaaa                                                >  1:1087198/1‑100 (MQ=255)
                                                 aCCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGaaaa                                               <  1:1354360/100‑1 (MQ=255)
                                                  ccAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAAt                                              <  2:1672316/100‑1 (MQ=255)
                                                   cAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAAtt                                             >  2:804706/1‑100 (MQ=255)
                                                    aaCTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATta                                            >  1:318514/1‑100 (MQ=255)
                                                      cTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATtata                                          <  1:65023/100‑1 (MQ=255)
                                                        ggATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAAc                                        <  1:873157/100‑1 (MQ=255)
                                                         gATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAAcc                                       <  1:462318/100‑1 (MQ=255)
                                                         gATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAAcc                                       <  1:1037279/100‑1 (MQ=255)
                                                         gATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAAcc                                       <  2:1175056/100‑1 (MQ=255)
                                                          aTACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCg                                      <  2:864331/100‑1 (MQ=255)
                                                           tACAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCgt                                     >  1:170701/1‑100 (MQ=255)
                                                             cAGAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCgttt                                   >  2:1233892/1‑100 (MQ=255)
                                                              cttccgatctaCTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCgtttg                                  <  1:509413/90‑1 (MQ=255)
                                                               gAAACAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCgtttgt                                 >  2:1030113/1‑100 (MQ=255)
                                                                 aaCAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCgtttgttt                               >  1:1277239/1‑100 (MQ=255)
                                                                   cAATAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGttttt                             >  1:1090986/1‑100 (MQ=255)
                                                                      tAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTAcc                          <  2:601474/100‑1 (MQ=255)
                                                                      tAACTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTAcc                          <  1:1603617/100‑1 (MQ=255)
                                                                       aaCTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCa                         <  2:78319/100‑1 (MQ=255)
                                                                        aCTATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCgtttgagatcggaag                        >  2:509412/1‑90 (MQ=255)
                                                                          tATTAGTTATGAATTTATCCTCTGTCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAAt                      >  2:667554/1‑100 (MQ=255)
                                                                          tATTAGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAAt                      >  2:2018465/1‑100 (MQ=255)
                                                                              aGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaa                  <  1:883656/100‑1 (MQ=255)
                                                                              aGTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaa                  >  2:205202/1‑100 (MQ=255)
                                                                               gTTATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaa                 >  2:1444734/1‑100 (MQ=255)
                                                                                ttATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaaa                >  2:492064/1‑100 (MQ=255)
                                                                                 tATGAATTTATCCTCTCTCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaaaa               <  2:1193202/100‑1 (MQ=255)
                                                                                 tATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaaaa               <  1:727332/100‑1 (MQ=255)
                                                                                 tATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaaaa               >  1:1507007/1‑100 (MQ=255)
                                                                                 tATGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaaaa               >  2:1589871/1‑100 (MQ=255)
                                                                                  aTGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaaaaa              >  1:1598271/1‑100 (MQ=255)
                                                                                  aTGAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCaaaaaa              <  1:1233898/100‑1 (MQ=255)
                                                                                    gAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAAcc            <  1:1626117/100‑1 (MQ=255)
                                                                                    gAATTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAAcc            <  2:5272/100‑1 (MQ=255)
                                                                                     aaTTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACca           >  1:1452614/1‑100 (MQ=255)
                                                                                     aaTTTATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACca           <  2:1087193/100‑1 (MQ=255)
                                                                                       tttATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACcaaa         >  2:1340856/1‑100 (MQ=255)
                                                                                        ttATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACcaaac        <  1:1589883/100‑1 (MQ=255)
                                                                                         tATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACcaaaca       <  1:1447035/100‑1 (MQ=255)
                                                                                         tATCCTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACcaaaca       <  1:1445290/100‑1 (MQ=255)
                                                                                            ccTCTATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACCAAACAaat    >  1:532782/1‑100 (MQ=255)
                                                                                              tctATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACCAAACAaataa  >  1:381810/1‑100 (MQ=255)
                                                                                              tctATCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACCAAACAaataa  >  2:1014399/1‑100 (MQ=255)
                                                                                                 |                                                                                                
CAACTAAGAGGCGCTTTTTTATCGGCTATTCATCACCAGATCATTGAAAACCAACTGGATACAGAAACAATAACTATTAGTTATGAATTTATCCTCTGTCAACATCTTATCGCAAATACCGAGTTCAGCTATTTGGCACTCCCTGAAAATTATAACCGTTTGTTTTTACCAAATTCAAAAAACCAAACAAATAA  >  NC_000913/3582175‑3582368

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A