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 2,595,306 C→A 30.8% intergenic (‑11/+2) arsC ← / ← arsB arsenate reductase/arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,3060CA30.8% 257.6 / 98.6 149intergenic (‑11/+2)arsC/arsBarsenate reductase/arsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base C (54/49);  new base A (24/22);  total (78/71)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

Only 100 of 161 total aligned reads displayed.

TCCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCAT  >  minE/2595237‑2595373
                                                                     |                                                                   
tcCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                    >  1:3971266/1‑71 (MQ=255)
tcCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                    >  1:5332946/1‑71 (MQ=255)
tcCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                    >  1:454615/1‑71 (MQ=255)
tcCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                    >  1:4863711/1‑71 (MQ=255)
  cAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCAt                                                                   >  1:2904947/1‑70 (MQ=255)
  cAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCAt                                                                   >  1:557149/1‑70 (MQ=255)
    gCGTGTTGCGTGAGGTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTa                                                                 >  1:512151/1‑70 (MQ=255)
    gCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                    <  1:3064936/67‑1 (MQ=255)
     cGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGTTAATGTTGCTCATATCAGTATCTCATTAc                                                                >  1:2334989/1‑70 (MQ=255)
     cGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTAc                                                                >  1:3241682/1‑70 (MQ=255)
     cGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACa                                                               <  1:2069308/71‑1 (MQ=255)
      gTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACaa                                                              <  1:1465342/71‑1 (MQ=255)
       tATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACa                                                               <  1:877463/69‑1 (MQ=255)
       tATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACa                                                               <  1:1366060/69‑1 (MQ=255)
         ttACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCAtt                                                                  >  1:1536322/1‑64 (MQ=255)
         ttACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGt                                                           >  1:5286726/1‑71 (MQ=255)
           aCGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTg                                                          >  1:3929362/1‑70 (MQ=255)
              cgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTg                                                          >  1:2678063/1‑67 (MQ=255)
              cgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGa                                                         >  1:4694044/1‑68 (MQ=255)
              cgACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGa                                                         >  1:1196369/1‑68 (MQ=255)
                  gTGCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACagagag                                                  <  1:1930385/71‑1 (MQ=255)
                    gCCACAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACagagagc                                                 >  1:2612185/1‑69 (MQ=255)
                     ccGCAGGCGGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACg                                               <  1:4105189/71‑1 (MQ=255)
                      cacAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCgc                                              >  1:5072877/3‑70 (MQ=255)
                      cacAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCgc                                              >  1:3576424/3‑70 (MQ=255)
                      cacAGGCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCgc                                              <  1:3848867/69‑2 (MQ=255)
                       gCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTg                                                          <  1:4014259/58‑1 (MQ=255)
                          ggCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACaaa                                                             >  1:5233959/1‑52 (MQ=255)
                          ggCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACaaa                                                             >  1:4637427/1‑52 (MQ=255)
                          ggCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGaca                                                       <  1:4191044/58‑3 (MQ=255)
                          ggCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGaca                                                       <  1:586702/58‑3 (MQ=255)
                          ggCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGaca                                                       <  1:1664765/58‑3 (MQ=255)
                          ggCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACaa                                                              <  1:5605779/51‑1 (MQ=255)
                           gCCGGGTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGt                                                           >  1:960539/1‑53 (MQ=255)
                            ccGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                    >  1:2551138/1‑43 (MQ=255)
                            ccGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCa                                                                    >  1:2642026/1‑43 (MQ=255)
                               ggTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                   >  1:2444134/1‑57 (MQ=255)
                               ggTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                   >  1:1329552/1‑57 (MQ=255)
                                gTTGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAgc                                     <  1:3826773/70‑1 (MQ=255)
                                 ttGTGATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCgcc                                             <  1:1653857/61‑3 (MQ=255)
                                 ttGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgcgc                                   <  1:340183/71‑1 (MQ=255)
                                    tgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                     <  1:954753/50‑1 (MQ=255)
                                    tgATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                     <  1:2989208/50‑1 (MQ=255)
                                     gATAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggc                                >  1:4396535/1‑70 (MQ=255)
                                     gATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                     <  1:1982257/49‑1 (MQ=255)
                                     gATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                     <  1:37804/49‑1 (MQ=255)
                                      aTAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGt                                                           <  1:3648858/42‑1 (MQ=38)
                                      aTAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACag                                                      >  1:3007442/1‑47 (MQ=255)
                                      aTAGATGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACag                                                      >  1:3614619/1‑47 (MQ=255)
                                       tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                     <  1:3409390/47‑1 (MQ=255)
                                       tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                     <  1:4723629/47‑1 (MQ=255)
                                       tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAaga                                                     <  1:4106394/47‑1 (MQ=255)
                                       tAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccag                             <  1:2410854/71‑1 (MQ=255)
                                        agaTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAg                                      <  1:5335149/59‑1 (MQ=255)
                                        aaaTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccagc                            >  1:3469632/1‑71 (MQ=255)
                                        aaaTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagccagc                            >  1:3462899/1‑71 (MQ=255)
                                         gaTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                            <  1:3367669/69‑2 (MQ=255)
                                          aTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGTGCCAGCGCAGCCAGCGt                          >  1:4839064/1‑71 (MQ=255)
                                          aTGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGt                          <  1:5387995/71‑1 (MQ=255)
                                          aTGGTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAgcg                                    >  1:544843/1‑61 (MQ=255)
                                           tGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTc                         <  1:5228961/71‑1 (MQ=255)
                                            ggTAATGTTGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGtga                        >  1:2836887/1‑69 (MQ=255)
                                              tAATGTTGCTCATATCAGTATCTAATTACAAAGTGACagaga                                                   <  1:439243/42‑1 (MQ=38)
                                               aaTGTTGCTCATATCAGTATCTCATTACAAAGTGAAagaga                                                   >  1:1638765/1‑41 (MQ=255)
                                               aaTGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTcaca                      >  1:1251148/1‑70 (MQ=255)
                                                 tGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagc                                <  1:155170/58‑1 (MQ=255)
                                                  gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagc                                >  1:4469462/1‑57 (MQ=255)
                                                  gTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGcagc                                >  1:2162843/1‑57 (MQ=255)
                                                   ttGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAg                 >  1:287879/1‑71 (MQ=255)
                                                   ttGCTCATATCAGTATCTAATTACAAAGTGACagag                                                    >  1:5415446/1‑36 (MQ=37)
                                                   ttGCTCATATCAGTATCTAATTACAAAGTGACagag                                                    >  1:3693737/1‑36 (MQ=37)
                                                   ttGCTCATATCAGTATCTAATTACAAAGTGACaga                                                     >  1:837759/1‑35 (MQ=37)
                                                   ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                  <  1:1086304/70‑1 (MQ=255)
                                                   ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                  <  1:5067645/70‑1 (MQ=255)
                                                   ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                  <  1:4281743/70‑1 (MQ=255)
                                                   ttGCTCATATCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACa                  <  1:3899196/70‑1 (MQ=255)
                                                      cTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGcac              <  1:844464/71‑1 (MQ=255)
                                                      cTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGca               <  1:1061871/70‑1 (MQ=255)
                                                         atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                  <  1:5688686/64‑1 (MQ=255)
                                                         atatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                  <  1:2459377/64‑1 (MQ=255)
                                                          tatCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAgc                                     <  1:5650733/44‑1 (MQ=255)
                                                          tatCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggcca                              <  1:4603532/51‑1 (MQ=255)
                                                          tatCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggcca                              <  1:4323806/51‑1 (MQ=255)
                                                           atCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACa                  >  1:2065172/1‑62 (MQ=255)
                                                           atCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggcca                              >  1:2786411/1‑50 (MQ=255)
                                                            tCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTc                         >  1:2403905/1‑54 (MQ=255)
                                                            tCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggcag        >  1:4892038/1‑71 (MQ=255)
                                                            tCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggca         <  1:1831062/70‑1 (MQ=255)
                                                            tCAGTATCTAATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccaga                            >  1:124132/1‑50 (MQ=255)
                                                              aGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAggg      <  1:977500/71‑1 (MQ=255)
                                                                tATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGca               <  1:3053832/60‑1 (MQ=255)
                                                                  tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTcaca                      <  1:2242025/51‑1 (MQ=255)
                                                                  tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACaaa                    >  1:4709551/1‑53 (MQ=255)
                                                                  tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAg                 >  1:3134278/1‑56 (MQ=255)
                                                                  tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAg                 >  1:705235/1‑56 (MQ=255)
                                                                  tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggcag        <  1:3355540/65‑1 (MQ=255)
                                                                  tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCAcaggcag        <  1:4290259/65‑1 (MQ=255)
                                                                  tctcATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCAt  >  1:65953/1‑71 (MQ=255)
                                                                  tctaATTACAAAGTGACAGAGAGCCGCCACGCCAGCGcggccag                             <  1:2731350/44‑1 (MQ=12)
                                                                  tctaATTACAAAGTGACAGAGAGCCGCCACGCCAGCGCGGCCAGAGTGACAAACAGCACCGGCACAGTCAt  >  1:1518678/1‑71 (MQ=255)
                                                                     |                                                                   
TCCAGCGTATTACGCGACGTGCCGCAGGCCGGGTTGTGATAAATGGTAATGTTGCTCATATCAGTATCTCATTACAAAGTGAAAGAGAGACGTAGCGCCAGCGCAGCCAGCGTCACAAACAGCACAGGCAGGGTCAT  >  minE/2595237‑2595373

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