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 2,595,491 G→A 25.5% C369C (TGC→TGT)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,4910GA25.5% 257.1 / 91.7 153C369C (TGC→TGT) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base G (51/62);  new base A (25/14);  total (77/76)
Fisher's exact test for biased strand distribution p-value = 6.25e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.53e-02

Only 100 of 158 total aligned reads displayed.

TCTGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGAC  >  minE/2595421‑2595560
                                                                      |                                                                     
tctGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCg                                                                       >  1:855357/1‑71 (MQ=255)
   gCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAg                                                                    >  1:2687148/1‑71 (MQ=255)
    cGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGc                                                                      <  1:2793191/68‑1 (MQ=255)
     gAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGc                                                                   >  1:3121949/1‑70 (MQ=255)
      aaaGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCa                                                                 <  1:1807966/71‑1 (MQ=255)
       aaGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCaa                                                                <  1:3251813/71‑1 (MQ=255)
       aaGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCaa                                                                <  1:4062936/71‑1 (MQ=255)
        aGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAAt                                                               >  1:3615097/1‑71 (MQ=255)
        aGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAAt                                                               >  1:4120768/1‑71 (MQ=255)
          tACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATca                                                             <  1:2745415/71‑1 (MQ=255)
           acatGCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATca                                                             >  1:1514912/4‑70 (MQ=255)
             gTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACAt                                                          <  1:4778729/71‑1 (MQ=255)
             atGCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACAt                                                          <  1:3814260/70‑1 (MQ=255)
              tGCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACAt                                                          >  1:665170/1‑70 (MQ=255)
               gCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTg                                                        >  1:528571/1‑71 (MQ=255)
                  gCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACAtt                                                         <  1:3803179/67‑1 (MQ=255)
                    cAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATa                                                   <  1:1972875/71‑1 (MQ=255)
                     agagTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATaa                                                  <  1:4839785/71‑1 (MQ=255)
                     agagTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATa                                                   >  1:2716251/1‑70 (MQ=255)
                       agTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAc                                                <  1:5198531/71‑1 (MQ=255)
                        gtagcgtagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAc                                                >  1:5664621/1‑70 (MQ=255)
                              ttgcCAGACTGCCAACCGGGGTGATTTTCGGGCCTAAATCACAGCCAATcac                                                            <  1:5169098/50‑1 (MQ=255)
                              tagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATcac                                                            <  1:3148925/52‑1 (MQ=255)
                              tagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATcac                                                            <  1:3109399/52‑1 (MQ=255)
                              tagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCAt                                             <  1:5261264/67‑1 (MQ=255)
                              tagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCAt                                             <  1:2479251/67‑1 (MQ=255)
                               agcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGct                                         >  1:117541/1‑70 (MQ=255)
                               agcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAACCGCAGCCAATCACATTGGCATAAACCATCGctt                                        >  1:1749143/1‑71 (MQ=255)
                                gcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATa                                                   <  1:4551350/59‑1 (MQ=255)
                                gcCAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTg                                                        >  1:830136/1‑54 (MQ=255)
                                 ccAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAcc                                               <  1:1278617/62‑1 (MQ=255)
                                  cAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATaaa                                                 >  1:725078/1‑59 (MQ=255)
                                   aGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCttt                                    <  1:1136169/71‑1 (MQ=255)
                                     gCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGa                                  >  1:3076353/1‑71 (MQ=255)
                                     gCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGa                                  >  1:44154/1‑71 (MQ=255)
                                      ctgccAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGcctct                                      >  1:5456389/4‑66 (MQ=255)
                                      cTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATca                                                             <  1:2849464/43‑1 (MQ=255)
                                       tgccAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATca                                                             <  1:5408309/40‑1 (MQ=16)
                                       tACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGAt                                 >  1:2367820/1‑70 (MQ=255)
                                         ccAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATc                                            <  1:4385994/57‑1 (MQ=255)
                                         ccAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAAc                              >  1:3451052/1‑71 (MQ=255)
                                          cAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATcaca                                                           <  1:2562623/41‑1 (MQ=255)
                                           aaTCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCa                                              >  1:1377362/1‑53 (MQ=255)
                                           aaTCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                            <  1:2905130/71‑1 (MQ=255)
                                            atcggggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                            <  1:97747/67‑1 (MQ=255)
                                             ttGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAcc                                               <  1:5342575/50‑1 (MQ=255)
                                             ttGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGc                            >  1:3748577/1‑69 (MQ=255)
                                             tcggggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCa                                              >  1:2381800/3‑51 (MQ=255)
                                              tGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGc                            >  1:4094631/1‑68 (MQ=255)
                                               ggggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAgt                        >  1:1923256/1‑70 (MQ=255)
                                               ggggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAg                         <  1:3745095/70‑1 (MQ=255)
                                               ggggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATaaa                                                 >  1:1519117/1‑46 (MQ=255)
                                               ggggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAc                                                <  1:4203771/47‑1 (MQ=255)
                                               ggggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGcttctt                                     >  1:2215367/1‑58 (MQ=255)
                                               ggggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATaa                               >  1:1869377/1‑64 (MQ=255)
                                               ggggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATaa                               >  1:623043/1‑64 (MQ=255)
                                               ggggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGc                            >  1:4763680/1‑67 (MQ=255)
                                               ggggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGc                            >  1:4738066/1‑67 (MQ=255)
                                                gggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAgtc                       >  1:3301054/1‑69 (MQ=255)
                                                 ggTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGAt                                 <  1:1616517/60‑1 (MQ=255)
                                                  gTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTg                                   <  1:4444327/57‑1 (MQ=255)
                                                   tAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc                    >  1:4639318/1‑71 (MQ=255)
                                                   tAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc                    <  1:848510/71‑1 (MQ=255)
                                                    aaTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATa                                                   <  1:5461221/39‑1 (MQ=255)
                                                     aTTTTCGGTCCCAAATCTCAGCCAATCACATTGGCATAAACAATCTATTCTTTGATAACGCCAGATGcc                    >  1:5660729/1‑69 (MQ=255)
                                                     aTTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                            <  1:3192559/61‑1 (MQ=255)
                                                      ttttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGt                  <  1:2214288/70‑1 (MQ=255)
                                                      ttttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGt                  <  1:3674096/70‑1 (MQ=255)
                                                      ttttCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGta                 >  1:3302211/1‑70 (MQ=255)
                                                       tttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATa                                <  1:1283530/55‑1 (MQ=255)
                                                       tttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgc                >  1:2993080/1‑71 (MQ=255)
                                                       tttCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGtac                >  1:4252284/1‑69 (MQ=255)
                                                            gTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCttt                                    <  1:1582934/46‑1 (MQ=255)
                                                            gTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGcc                           >  1:1162773/1‑55 (MQ=255)
                                                             tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAt          >  1:5619693/1‑71 (MQ=255)
                                                              cctaaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTc         <  1:2033291/68‑1 (MQ=255)
                                                              cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc                    >  1:50638/1‑60 (MQ=255)
                                                              cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc                    >  1:3994363/1‑60 (MQ=255)
                                                              cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc                    >  1:3866857/1‑60 (MQ=255)
                                                              cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAt          >  1:763433/1‑70 (MQ=255)
                                                               ctaaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTc         >  1:2891717/3‑70 (MQ=255)
                                                               ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCttt                                    <  1:5252944/43‑1 (MQ=255)
                                                               ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc         <  1:3367170/70‑1 (MQ=255)
                                                               ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc         <  1:5299032/70‑1 (MQ=255)
                                                               ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc         <  1:3949922/70‑1 (MQ=255)
                                                               ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc         <  1:1722350/70‑1 (MQ=255)
                                                                taaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCaa       >  1:3565030/2‑71 (MQ=255)
                                                                cAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCaa       <  1:3422265/71‑1 (MQ=255)
                                                                 aaaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgc                >  1:1087065/1‑61 (MQ=255)
                                                                 aaaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAAt      <  1:4455755/71‑1 (MQ=255)
                                                                 aaaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAAt      >  1:2927406/1‑71 (MQ=255)
                                                                 aaaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAAt      >  1:4870513/1‑71 (MQ=255)
                                                                  aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCg                   <  1:2150286/57‑1 (MQ=255)
                                                                  aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCg                   <  1:131323/57‑1 (MQ=255)
                                                                  aaTCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg     <  1:334155/71‑1 (MQ=255)
                                                                  aaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAtc     <  1:5437133/71‑2 (MQ=255)
                                                                  aaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAtc     <  1:911476/71‑2 (MQ=255)
                                                                    tCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGAt                                 <  1:138087/41‑1 (MQ=255)
                                                                      gCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGAc  <  1:871666/70‑1 (MQ=255)
                                                                      gCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGAc  <  1:3386210/70‑1 (MQ=255)
                                                                      |                                                                     
TCTGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGAC  >  minE/2595421‑2595560

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