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
A6 F1 I0 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,571,330 T→C 29.2% intergenic (+98/‑1681) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,571,3300TC29.2% 193.7 / 99.2 137intergenic (+98/‑1681)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (46/51);  new base C (21/19);  total (67/70)
Fisher's exact test for biased strand distribution p-value = 7.07e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.67e-01

Only 100 of 143 total aligned reads displayed.

CTCCTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATG  >  minE/2571261‑2571398
                                                                      |                                                                      
  ccTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATg                                                                     >  1:2843252/1‑71 (MQ=255)
     tGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGt                                                                    >  1:4428264/1‑69 (MQ=255)
             cTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                          >  1:901165/1‑71 (MQ=255)
             cTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                          <  1:4524869/71‑1 (MQ=255)
               aaTTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      >  1:2212674/1‑71 (MQ=255)
                attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATg                                                                     >  1:486374/1‑57 (MQ=255)
                attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      <  1:1810774/70‑1 (MQ=255)
                attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      <  1:4295718/70‑1 (MQ=255)
                 ttattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGt                                                            <  1:4140373/65‑1 (MQ=255)
                 ttattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGt                                                            <  1:1623633/65‑1 (MQ=255)
                  tattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                                   >  1:1101002/1‑71 (MQ=255)
                   attTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                                   >  1:2657581/1‑70 (MQ=255)
                   attTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                                   >  1:2151432/1‑70 (MQ=255)
                    tttttGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                                   >  1:3723745/1‑69 (MQ=255)
                            tatTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctc                                         >  1:2722097/1‑71 (MQ=255)
                             atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      <  1:3553326/57‑1 (MQ=255)
                             atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      <  1:3364244/57‑1 (MQ=255)
                             atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGa                                                    >  1:4371958/1‑59 (MQ=255)
                             atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctct                                        >  1:4021442/1‑71 (MQ=255)
                             atTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctct                                        >  1:5669681/1‑71 (MQ=255)
                              ttACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTtaataa                                                              >  1:4959213/1‑50 (MQ=255)
                              ttACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCtctc                                       <  1:2285486/71‑1 (MQ=255)
                                 cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTTTGTTAATAAGTTc                                                          <  1:687733/51‑1 (MQ=255)
                                 cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑gca                                                    >  1:5408570/1‑53 (MQ=255)
                                  ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGt                                                            <  1:5675227/48‑1 (MQ=255)
                                  ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      <  1:284437/52‑1 (MQ=255)
                                  ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      <  1:1216093/52‑1 (MQ=255)
                                    cATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGa                                                 <  1:1926925/55‑1 (MQ=255)
                                    cATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGa                                 >  1:2016698/1‑71 (MQ=255)
                                     aTTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAt                                <  1:327776/71‑1 (MQ=255)
                                      ttAGCTTCGATGATTTTT‑CTTTAATATTCATTATGtt                                                                   >  1:5005218/1‑37 (MQ=255)
                                      ttAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAtt                               >  1:598891/1‑71 (MQ=255)
                                       tAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGTAtt                               <  1:225473/70‑1 (MQ=255)
                                        aGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAttt                              <  1:2451652/70‑1 (MQ=255)
                                             tgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGAtttctt                           <  1:4252406/69‑1 (MQ=255)
                                             tgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTC‑t                                                        <  1:4702250/40‑1 (MQ=12)
                                             cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                          <  1:4416152/39‑1 (MQ=255)
                                             cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑t                                                        >  1:3069491/1‑40 (MQ=255)
                                             cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑t                                                        >  1:4491163/1‑40 (MQ=255)
                                              gatgatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                       <  1:1022779/71‑1 (MQ=255)
                                               atgatTTTTCCTTTAATATCCAGCATGTTaagaag                                                             >  1:1241167/1‑35 (MQ=9)
                                               atgatTTTTCCTTTAATATCCAGCATGTTaagaag                                                             >  1:4082362/1‑35 (MQ=9)
                                               atgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTc                                                          <  1:2605981/38‑1 (MQ=12)
                                               atgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTc                                                          <  1:3842416/38‑1 (MQ=12)
                                               atgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATc                        >  1:3425292/1‑71 (MQ=255)
                                               atgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTC‑T‑gg                                                     >  1:1356806/1‑41 (MQ=16)
                                               atgatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCAtt                                    <  1:1042987/57‑1 (MQ=255)
                                                 gatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                       <  1:3671395/68‑1 (MQ=255)
                                                 gatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTc                    >  1:3264253/1‑71 (MQ=255)
                                                 gatTTTA‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTc                    >  1:734041/1‑71 (MQ=255)
                                                 gatATTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                      >  1:5530527/1‑37 (MQ=255)
                                                  tttttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTc                    >  1:5093691/2‑71 (MQ=255)
                                                   ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                            <  1:1745162/45‑1 (MQ=255)
                                                   ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                            <  1:720328/45‑1 (MQ=255)
                                                   ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                            <  1:4008930/45‑1 (MQ=255)
                                                   ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCtt                  <  1:119029/71‑1 (MQ=255)
                                                    tttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCtt                  >  1:2110719/1‑71 (MQ=255)
                                                     ttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTg                 <  1:4212067/70‑1 (MQ=255)
                                                     ttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTg                 <  1:3487164/70‑1 (MQ=255)
                                                      ttccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCtt                  <  1:1754179/67‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                 <  1:2989061/68‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                 <  1:4726710/68‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                 <  1:529762/68‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                 <  1:2353435/68‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                 <  1:4254032/68‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                 <  1:4309757/68‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                 <  1:1522883/68‑1 (MQ=255)
                                                       tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg                 <  1:2759612/68‑1 (MQ=255)
                                                       t‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt               <  1:5695919/70‑1 (MQ=255)
                                                         cTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt               <  1:5031128/69‑1 (MQ=255)
                                                         cTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt             >  1:4191709/1‑71 (MQ=255)
                                                         cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc              >  1:1524999/1‑71 (MQ=255)
                                                         cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc              <  1:116806/71‑1 (MQ=255)
                                                         cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc              >  1:4842888/1‑71 (MQ=255)
                                                          tttAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg                 <  1:5480766/67‑1 (MQ=255)
                                                            tAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGcc          >  1:837254/1‑71 (MQ=255)
                                                            tAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGcc          >  1:109743/1‑71 (MQ=255)
                                                            tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTa                          >  1:4814237/1‑56 (MQ=255)
                                                            tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTa                          >  1:2221760/1‑56 (MQ=255)
                                                            tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCt             >  1:3759709/1‑69 (MQ=255)
                                                            tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc           >  1:5528958/1‑71 (MQ=255)
                                                            tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc           >  1:3672754/1‑71 (MQ=255)
                                                            tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc           >  1:2356605/1‑71 (MQ=255)
                                                            tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc           >  1:4743825/1‑71 (MQ=255)
                                                             aaTATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt             <  1:2164482/67‑1 (MQ=255)
                                                              atatTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCg         <  1:1877765/70‑1 (MQ=255)
                                                                 ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATc                        >  1:5095556/1‑52 (MQ=255)
                                                                 ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATc                        >  1:4038816/1‑52 (MQ=255)
                                                                 ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt             <  1:1611576/63‑1 (MQ=255)
                                                                 ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAgt     <  1:5305193/71‑2 (MQ=255)
                                                                 ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg      <  1:1864496/70‑1 (MQ=255)
                                                                 ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg      <  1:3328060/70‑1 (MQ=255)
                                                                   cATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt   >  1:2803109/1‑71 (MQ=255)
                                                                    aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                       >  1:482338/1‑50 (MQ=255)
                                                                    aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt   <  1:3930766/70‑1 (MQ=255)
                                                                    aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATg  <  1:4985725/71‑1 (MQ=255)
                                                                    aTTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTATATCCGTCTTGTTCTGCCGCAGGAt   <  1:5026670/70‑1 (MQ=255)
                                                                     ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTa                          <  1:398453/46‑1 (MQ=255)
                                                                     ttATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt               <  1:127074/57‑1 (MQ=255)
                                                                      tATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGAt   >  1:5231582/1‑68 (MQ=255)
                                                                      |                                                                      
CTCCTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAGGATG  >  minE/2571261‑2571398

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A