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 2,571,326 T→C 31.2% intergenic (+94/‑1685) yibH → / → ysaB hypothetical protein/hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,571,3260TC31.2% 168.8 / 102.0 128intergenic (+94/‑1685)yibH/ysaBhypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (44/44);  new base C (21/19);  total (65/63)
Fisher's exact test for biased strand distribution p-value = 8.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.47e-01

Only 100 of 139 total aligned reads displayed.

TGCTCCTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAG  >  minE/2571259‑2571394
                                                                    |                                                                      
  cTCCTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCAtt                                                                    <  1:3430721/70‑1 (MQ=255)
    ccTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATg                                                                 >  1:2843252/1‑71 (MQ=255)
     cTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATAtt                                                                        >  1:1725519/1‑63 (MQ=255)
     cTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGt                                                                >  1:1917431/1‑71 (MQ=255)
       tGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGt                                                                >  1:3885188/1‑69 (MQ=255)
       tGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGt                                                                >  1:4428264/1‑69 (MQ=255)
        gTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGtt                                                               <  1:5048383/69‑1 (MQ=255)
               cTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                      <  1:4524869/71‑1 (MQ=255)
               cTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                      >  1:901165/1‑71 (MQ=255)
                tAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCa                                                                      <  1:4300056/54‑1 (MQ=255)
                  attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  <  1:4483016/70‑1 (MQ=255)
                  attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  <  1:4295718/70‑1 (MQ=255)
                  attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  >  1:3597404/1‑70 (MQ=255)
                  attattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  <  1:1810774/70‑1 (MQ=255)
                   ttattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGt                                                        <  1:1623633/65‑1 (MQ=255)
                    tattTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                               >  1:1101002/1‑71 (MQ=255)
                     attTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCAt                                                                     >  1:1810523/1‑50 (MQ=255)
                      tttttGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGAt                                               >  1:3723745/1‑69 (MQ=255)
                            cATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                        <  1:4267138/70‑1 (MQ=255)
                              tatTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctc                                     >  1:2722097/1‑71 (MQ=255)
                              tatTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGctc                                     >  1:2352113/1‑71 (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‑GGa                                                >  1:4377557/1‑59 (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)
                                   cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                      <  1:4607018/51‑1 (MQ=255)
                                   cTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑gca                                                >  1:5408570/1‑53 (MQ=255)
                                    ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGt                                                        <  1:5675227/48‑1 (MQ=255)
                                    ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  <  1:1216093/52‑1 (MQ=255)
                                    ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  <  1:284437/52‑1 (MQ=255)
                                    ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  <  1:5198668/52‑1 (MQ=255)
                                    ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑g                                                  <  1:692641/52‑1 (MQ=255)
                                    ttCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATg                                              <  1:5365132/56‑1 (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‑GGAt                                               >  1:1240828/1‑51 (MQ=255)
                                        ttAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGAtt                           >  1:4836689/1‑71 (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)
                                             ttCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGa                                             >  1:4025417/1‑48 (MQ=255)
                                               tgatgatTTTTCCTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGAtttctt                       <  1:4252406/69‑1 (MQ=255)
                                               cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTc                                                      <  1:4416152/39‑1 (MQ=255)
                                               cGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑t                                                    >  1:3069491/1‑40 (MQ=255)
                                                gatgatTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATcc                   <  1:1022779/71‑1 (MQ=255)
                                                 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‑g                                                  >  1:4875433/1‑37 (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)
                                                    atTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGa                                                >  1:3172798/1‑38 (MQ=255)
                                                    atTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCtctc                                   <  1:2802838/51‑1 (MQ=255)
                                                     ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                        <  1:4008930/45‑1 (MQ=255)
                                                     ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                        <  1:1745162/45‑1 (MQ=255)
                                                     ttttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGtgtg                                        <  1:720328/45‑1 (MQ=255)
                                                     ttttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCt               >  1:1490904/1‑71 (MQ=255)
                                                      tttc‑CTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCtt              >  1:2110719/1‑71 (MQ=255)
                                                       ttt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTg             <  1:4212067/70‑1 (MQ=255)
                                                        tt‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTa                      >  1:2233766/1‑60 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg             <  1:327799/68‑1 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg             <  1:529762/68‑1 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg             <  1:2033084/68‑1 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg             <  1:2989061/68‑1 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg             <  1:4726710/68‑1 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg             <  1:5635651/68‑1 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTg             <  1:2353435/68‑1 (MQ=255)
                                                         tccTTTAATATCCAGCATGTTAAGAAGTTC‑TGGGATAGCTGTAATCTCATTAGATTTCTCATCCGTCTTg             <  1:1522883/68‑1 (MQ=255)
                                                           cTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGtt           <  1:5031128/69‑1 (MQ=255)
                                                           cTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt         >  1:4191709/1‑71 (MQ=255)
                                                           cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc          >  1:4842888/1‑71 (MQ=255)
                                                           cTTTAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATc          <  1:116806/71‑1 (MQ=255)
                                                            tttAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTc          <  1:475903/69‑1 (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                      >  1:2221760/1‑56 (MQ=255)
                                                              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTgt       >  1:5697330/1‑70 (MQ=255)
                                                              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc       >  1:5528958/1‑71 (MQ=255)
                                                              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc       >  1:4743825/1‑71 (MQ=255)
                                                              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc       >  1:2674080/1‑71 (MQ=255)
                                                              tAATATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTGATCTGc       >  1:3672754/1‑71 (MQ=255)
                                                               aaTATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt         <  1:2164482/67‑1 (MQ=255)
                                                               aaTATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTgat           >  1:2205858/1‑64 (MQ=255)
                                                               aaTATCCAGCATGTTAAGAAGTTCAG‑GGATAGCTGTGATCTCATTGGATTTCTTATCCGTCTTgat           >  1:3672967/1‑64 (MQ=255)
                                                                atatTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCg     <  1:1877765/70‑1 (MQ=255)
                                                                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATc                    >  1:4038816/1‑52 (MQ=255)
                                                                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt         <  1:1716614/63‑1 (MQ=255)
                                                                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt         <  1:1611576/63‑1 (MQ=255)
                                                                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCt         <  1:2512567/63‑1 (MQ=255)
                                                                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg  <  1:1864496/70‑1 (MQ=255)
                                                                   ttCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAg  <  1:1175257/70‑1 (MQ=255)
                                                                    |                                                                      
TGCTCCTTGTAAGGACTAATTATTTTTGCATATTACTTCATTAGCTTCGATGATTTTT‑CTTTAATATTCATTATGTTAATAAGTTC‑T‑GGATGAGTGTGCTCTCATTGGATTTTTTATCCGTCTTGTTCTGCCGCAG  >  minE/2571259‑2571394

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