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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,485,588 G→A 37.6% G220G (GGC→GGT)  yidC ← cytoplasmic insertase into membrane protein, Sec system

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,485,5880GA37.6% 59.9 / 60.0 98G220G (GGC→GGT) yidCcytoplasmic insertase into membrane protein, Sec system
Reads supporting (aligned to +/- strand):  ref base G (14/47);  new base A (27/10);  total (41/57)
Fisher's exact test for biased strand distribution p-value = 1.86e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.28e-01

GGTATCGAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATG  >  minE/2485537‑2485651
                                                   |                                                               
ggTATCGAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAg                                                <  1:195723/69‑1 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:1347468/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:1342253/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:2276306/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:2739087/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:2976137/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:2193331/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:2034384/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:1889305/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:825421/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:1084689/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:851708/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:1058161/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:853311/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTg                                              >  1:1583119/1‑68 (MQ=255)
   aTCGAACTTGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCAGCACCACGGAAGGTGTGCAGt                                               >  1:2640702/1‑67 (MQ=255)
    tCGAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCg                                            <  1:95687/69‑1 (MQ=255)
    tCGAACTTGTATTTCTCATACTTCTCGTAAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCg                                            <  1:3346525/69‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:252357/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:2313186/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:2716885/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:2230620/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:318536/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:3302029/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:608173/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:1036267/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:1630260/68‑1 (MQ=255)
      gAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGa                                           <  1:1406621/68‑1 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:253073/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:3049335/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:3278155/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:852320/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:1503395/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:33654/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:798003/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtgc                                     >  1:1121028/1‑69 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtg                                      >  1:2206610/1‑68 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtg                                      >  1:2734114/1‑68 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtg                                      >  1:470712/1‑68 (MQ=255)
           tGTATTTCTCGTACTTCTCGTCAGGCGTGGAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTtg                                      >  1:1494616/1‑68 (MQ=255)
                 tctcATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTc                               >  1:2379307/1‑69 (MQ=255)
                 tctcATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTc                               >  1:1677448/1‑69 (MQ=255)
                 tctcATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTc                               >  1:1721891/1‑69 (MQ=255)
                 tctcATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTc                               >  1:2316345/1‑69 (MQ=255)
                 tctcATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTc                               >  1:857838/1‑69 (MQ=255)
                 tctcATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTc                               >  1:2242966/1‑69 (MQ=255)
                 tctcATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGATGCTGCtt                                >  1:2482961/1‑68 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1058193/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:3321213/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1100808/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:79355/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:12117/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:947471/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1231220/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:2808495/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1027142/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:2775808/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1304129/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:484211/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1418596/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1737303/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1739052/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:2072396/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:2139046/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1462383/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1367314/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:2654744/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:2532356/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:2431424/69‑1 (MQ=255)
                          tctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:1341582/69‑1 (MQ=255)
                           ctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCgag                     >  1:2098056/1‑69 (MQ=255)
                           ctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCgag                     >  1:3402669/1‑69 (MQ=255)
                           ctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCgag                     >  1:3300325/1‑69 (MQ=255)
                           ctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCgag                     >  1:2399735/1‑69 (MQ=255)
                           ctcGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCgag                     >  1:3142708/1‑69 (MQ=255)
                                        gattACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:241180/66‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:3299324/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:954696/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:2299977/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:33302/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:1168655/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:1834854/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:2103129/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:1524546/69‑1 (MQ=255)
                                        gAGTACGCCGCACCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCaga        <  1:1963582/69‑1 (MQ=255)
                                             cgccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGa    >  1:1052609/1‑68 (MQ=255)
                                             cgccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGa    >  1:1847183/1‑68 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCga                      <  1:413829/48‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:436061/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:2758290/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:689049/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:647067/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:1354594/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:392132/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:1316052/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:1172311/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:2967342/68‑1 (MQ=255)
                                               ccgcGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATg  <  1:2984672/68‑1 (MQ=255)
                                                   |                                                               
GGTATCGAACTTGTATTTCTCATACTTCTCGTCAGGCGTGGAGTACGCCGCGCCACGGAAGGTGTGCAGTGCGAAGTTGCTGCTTCCGGTATCGAGATGCGGTGGCAGAGTGATG  >  minE/2485537‑2485651

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A