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 2,596,157 G→T 31.9% A147A (GCC→GCA)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,596,1570GT31.9% 116.6 / 48.3 72A147A (GCC→GCA) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base G (16/33);  new base T (10/13);  total (26/46)
Fisher's exact test for biased strand distribution p-value = 4.35e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.23e-01

CCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGAACCCTAAAGCCAGCAGCA  >  minE/2596092‑2596224
                                                                 |                                                                   
ccgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCaa                                                                 <  1:4561973/67‑1 (MQ=255)
ccAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                                                <  1:61551/71‑1 (MQ=255)
 cgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAta                                                               <  1:1027594/69‑2 (MQ=255)
 cgaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAt                                                                >  1:568668/3‑70 (MQ=255)
  gaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAtaa                                                              <  1:2907473/70‑3 (MQ=255)
  gaagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAAtaa                                                              <  1:1074104/70‑3 (MQ=255)
  aaaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCa                                                                  <  1:254872/67‑1 (MQ=255)
  aaaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGa                                                              <  1:2147117/71‑1 (MQ=255)
   aagaagTCCGCCGAGACGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGc                                                                   <  1:2102362/65‑1 (MQ=255)
   aaGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGaa                                                             <  1:1532620/71‑1 (MQ=255)
    aGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAAt                                                            >  1:2210402/1‑71 (MQ=255)
    aGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAAt                                                            >  1:343780/1‑71 (MQ=255)
     gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATc                                                           <  1:1231880/71‑1 (MQ=255)
     gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATc                                                           <  1:1474192/71‑1 (MQ=255)
     gAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATc                                                           >  1:8113/1‑71 (MQ=255)
        aTCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCgg                                                        >  1:25208/1‑71 (MQ=255)
             aggAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGc                                                                   <  1:920563/54‑1 (MQ=255)
               gagaCGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCAt                                                 >  1:618636/4‑71 (MQ=255)
               gagaCGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCAt                                                 >  1:5038161/4‑71 (MQ=255)
               gAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                                                 <  1:332899/71‑1 (MQ=255)
               gAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                                                 <  1:5361754/71‑1 (MQ=255)
                   cGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACg                                             <  1:1992297/71‑1 (MQ=255)
                   cGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACg                                             <  1:5620776/71‑1 (MQ=255)
                   cGATATTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGAca                                             <  1:2088555/71‑2 (MQ=255)
                    gATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGgccgcc                                                   <  1:1043670/64‑1 (MQ=255)
                    gATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGa                                            <  1:1032259/71‑1 (MQ=255)
                    gATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGa                                            <  1:1039141/71‑1 (MQ=255)
                       atTCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATc                                                           >  1:2517566/1‑53 (MQ=255)
                        ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                                                <  1:5580356/47‑1 (MQ=255)
                        ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAAt                                                                <  1:86279/47‑1 (MQ=255)
                        ttCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGc                                        <  1:2205322/71‑1 (MQ=255)
                        ttCACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGc                                        <  1:2890870/71‑1 (MQ=255)
                        ttCACCAGCTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCAt                                                 <  1:2379629/62‑1 (MQ=255)
                          cACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGcc                                       <  1:5543577/70‑1 (MQ=255)
                          cACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGcc                                       <  1:4629170/70‑1 (MQ=255)
                          cACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGc                                        >  1:3401340/1‑69 (MQ=255)
                          cACCAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGcc                                       <  1:2777360/70‑1 (MQ=255)
                             cAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCg                                   <  1:1548326/71‑1 (MQ=255)
                             cAGGTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtg                                   >  1:3791224/1‑69 (MQ=255)
                              aGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                                                 >  1:3513260/1‑56 (MQ=255)
                              aGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCAt                                                 >  1:3866034/1‑56 (MQ=255)
                              aGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCa                                      >  1:2594433/1‑67 (MQ=255)
                               ggTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCg                                   >  1:4563082/1‑69 (MQ=255)
                               ggTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtgtc                                 >  1:2786185/1‑70 (MQ=255)
                               ggTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtgtc                                 >  1:1878442/1‑70 (MQ=255)
                                gTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGAcaa                                            <  1:4699307/59‑3 (MQ=255)
                                gTTAGAAACAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAgtg                                   <  1:204203/68‑3 (MQ=255)
                                   ggAGACAATAAGCGGCAGGCTGGCGGTATCGGaaa                                                                 >  1:995273/1‑35 (MQ=255)
                                    gagaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCg                                                         <  1:4551296/42‑1 (MQ=255)
                                    gagaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGcc                            <  1:2455605/71‑1 (MQ=255)
                                      gaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCtt                          <  1:2713506/71‑1 (MQ=255)
                                      gaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCtt                          <  1:1011863/71‑1 (MQ=255)
                                      gaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCtt                          <  1:5668941/71‑1 (MQ=255)
                                      gaCAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCtt                          <  1:3078189/71‑1 (MQ=255)
                                       aCAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATcct                                                         <  1:3834837/39‑2 (MQ=21)
                                       aCAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAGTGTCGTGccctg                         <  1:1373634/71‑4 (MQ=255)
                                       aCAATGAGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAGTGTCGTGccctg                         >  1:2704228/1‑68 (MQ=255)
                                        cAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCttt                         <  1:2081361/70‑1 (MQ=255)
                                        cAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCttt                         <  1:2206291/70‑1 (MQ=255)
                                           tAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACt                      >  1:3766970/1‑70 (MQ=255)
                                             aGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGaa                   <  1:679941/71‑1 (MQ=255)
                                             aGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGa                    <  1:3919204/70‑1 (MQ=255)
                                             aGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATAACGaa                                           >  1:2443821/1‑47 (MQ=255)
                                             aGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACaaa                                           >  1:4412467/1‑47 (MQ=255)
                                             aGCGGCAGGCTGGCCGTATCTGCAATAAATCCTGCAGCCATGACAAAGGCCAGTGTCGTGCCCTGGCTGaa                   >  1:1293074/1‑71 (MQ=255)
                                                     gCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGAACCCTAAAg           <  1:2946016/71‑1 (MQ=255)
                                                         gCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGAACCCTAAAGCcag       >  1:1390934/1‑71 (MQ=255)
                                                             tATCGGCAATTAATCCGGCCGCCATCACGAACGCCAGCGt                                  <  1:1241997/40‑1 (MQ=255)
                                                              aTCGGCAATGAATCCGGCCGCCATCACGAACGCCa                                      >  1:3517808/1‑35 (MQ=255)
                                                              aTCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAg                                >  1:788957/1‑41 (MQ=255)
                                                              aTCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGaa                   >  1:4666977/1‑54 (MQ=255)
                                                               tCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGAACCCTAAAGCCAgcagca  <  1:925310/70‑1 (MQ=255)
                                                                 ggCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGaa                   >  1:2865199/1‑51 (MQ=255)
                                                                 |                                                                   
CCAAAGAAATCAGCGGAAACGATATTCACCAGGTTGGAGACAATAAGCGGCAGGCTGGCGGTATCGGCAATGAATCCGGCCGCCATCACGAACGCCAGCGTAGTGCCTTTACTGAACCCTAAAGCCAGCAGCA  >  minE/2596092‑2596224

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