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 2,595,545 G→A 27.7% S351S (AGC→AGT)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,5450GA27.7% 248.0 / 104.8 159S351S (AGC→AGT) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base G (62/53);  new base A (28/16);  total (90/69)
Fisher's exact test for biased strand distribution p-value = 2.89e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.26e-01

Only 100 of 172 total aligned reads displayed.

TTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATAGAAGAGAGGAAGGCG  >  minE/2595476‑2595614
                                                                     |                                                                     
tttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgc                                                                      >  1:2993080/1‑71 (MQ=255)
tttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGACAGATGCCGtg                                                                       <  1:1286167/70‑1 (MQ=255)
  tCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgct                                                                     >  1:803359/1‑70 (MQ=255)
      tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAt                                                                >  1:5619693/1‑71 (MQ=255)
       cctaaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTc                                                               <  1:2033291/68‑1 (MQ=255)
       cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAt                                                                >  1:3396011/1‑70 (MQ=255)
       cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAt                                                                >  1:763433/1‑70 (MQ=255)
        ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc                                                               <  1:3367170/70‑1 (MQ=255)
        ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc                                                               <  1:5299032/70‑1 (MQ=255)
        ccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc                                                               <  1:1722350/70‑1 (MQ=255)
         taaaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCaa                                                             >  1:3565030/2‑71 (MQ=255)
         cAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCaa                                                             <  1:3422265/71‑1 (MQ=255)
           aaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAtc                                                           <  1:5437133/71‑2 (MQ=255)
           aaTCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAt                                                            >  1:2903195/1‑70 (MQ=255)
             tcacAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGa                                                         >  1:2392320/4‑71 (MQ=255)
             tCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGa                                                         >  1:4288879/1‑71 (MQ=255)
               acAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGa                                                         >  1:2101087/2‑69 (MQ=255)
               acAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGAc                                                        <  1:3159032/69‑1 (MQ=255)
               acAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGAc                                                        <  1:1526969/69‑1 (MQ=255)
               acAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACa                                                       <  1:214923/70‑1 (MQ=255)
                cAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAAt                                                            <  1:84031/65‑1 (MQ=255)
                cAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACaa                                                      <  1:770904/71‑1 (MQ=255)
                  gCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGcg                                                    >  1:4631505/1‑71 (MQ=255)
                  gCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAcg                                                    <  1:2923227/71‑1 (MQ=255)
                   ccAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAgcgc                                                   <  1:3262228/71‑1 (MQ=255)
                   ccAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgc                                                                      >  1:3954659/1‑52 (MQ=255)
                      aTCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGa                                                         >  1:595489/1‑62 (MQ=255)
                      aTCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGa                                                         >  1:2181547/1‑62 (MQ=255)
                      aTCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGcc                                                <  1:2079645/71‑1 (MQ=255)
                       tCACATTGGCATAAATCATTGCCTCTTTGACGCCGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCAcc                                                >  1:2467144/1‑70 (MQ=255)
                       tCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGa                                                         >  1:2594187/1‑61 (MQ=255)
                       tCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGa                                                         >  1:2221376/1‑61 (MQ=255)
                       tCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCa                                               <  1:2781269/71‑1 (MQ=255)
                         acaTTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAgcgca                                                  >  1:3832121/1‑65 (MQ=255)
                         acaTTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAgcgca                                                  >  1:223661/1‑65 (MQ=255)
                         acaTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAAc                                             <  1:3254161/71‑1 (MQ=255)
                         acaTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAAc                                             >  1:157761/1‑71 (MQ=255)
                         acaTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAAc                                             >  1:3459158/1‑71 (MQ=255)
                          caTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAAcc                                            <  1:1634087/71‑1 (MQ=255)
                          caTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAAc                                             <  1:1966156/70‑1 (MQ=255)
                           aTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGa                                                         >  1:5175147/1‑57 (MQ=255)
                           aTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGa                                                         >  1:168534/1‑57 (MQ=255)
                           aTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGa                                                         >  1:823567/1‑57 (MQ=255)
                           aTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAc                                                     <  1:2983404/61‑1 (MQ=255)
                           aTTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCa                                           <  1:4849085/71‑1 (MQ=255)
                            ttGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGtactc                                                                    >  1:2718459/1‑44 (MQ=255)
                            ttGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGTACTCCCGTCAAt                                                            >  1:5379357/1‑53 (MQ=255)
                            ttGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAg                                          <  1:1979696/71‑1 (MQ=255)
                             tGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCaa                                                             >  1:2678707/1‑51 (MQ=255)
                             tGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGa                                                         >  1:2541286/1‑55 (MQ=255)
                             tGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCaa                                              >  1:3055542/1‑66 (MQ=255)
                             tGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCaa                                              >  1:3920017/1‑66 (MQ=255)
                              ggCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCaa                                                             >  1:3308327/1‑50 (MQ=255)
                                  tAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATg                                                           <  1:135212/48‑1 (MQ=255)
                                  tAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGt                                    >  1:1124572/1‑71 (MQ=255)
                                   aaaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTAc                                       >  1:1249439/1‑67 (MQ=255)
                                   aaaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTAc                                       >  1:1088319/1‑67 (MQ=255)
                                   aaaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                                   >  1:2560031/1‑71 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACaa                                                      >  1:2762815/1‑51 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAcgcg                                                  >  1:611440/1‑55 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAcgcg                                                  >  1:5035245/1‑55 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                                   <  1:4005571/70‑1 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCg                                  >  1:4762948/1‑71 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCg                                  >  1:4571849/1‑71 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCg                                  >  1:1911825/1‑71 (MQ=255)
                                    aaCCATCGCTTCTTTGATAACGCCAGATGCCGAGCTGCCATCAATGGACAACGCGCCAAcc                                            >  1:4243777/1‑61 (MQ=255)
                                       cATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATc                                                               <  1:4131968/39‑1 (MQ=255)
                                        aTCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCaa                                                             >  1:4003632/1‑40 (MQ=255)
                                           gCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATAtt                           >  1:285528/1‑71 (MQ=255)
                                           gCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATAtt                           <  1:4176290/71‑1 (MQ=255)
                                               cttTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAAcgc                                                   <  1:5218190/43‑1 (MQ=255)
                                               cttTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGt                         <  1:1743118/69‑1 (MQ=255)
                                                tttGACGACGCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGtt                        <  1:1311838/69‑1 (MQ=255)
                                                 ttGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACgcgc                                                 >  1:367765/1‑43 (MQ=255)
                                                  tGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCat                     <  1:278853/70‑1 (MQ=255)
                                                   gATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCataa                   >  1:900912/1‑71 (MQ=255)
                                                   gATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCataa                   >  1:467426/1‑71 (MQ=255)
                                                    aTAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGt                         >  1:5610185/1‑64 (MQ=255)
                                                       aCGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATaga               <  1:1441744/71‑1 (MQ=255)
                                                       aCGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATaga               <  1:1448564/71‑1 (MQ=255)
                                                       aCGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATag                <  1:1061604/70‑1 (MQ=255)
                                                       aCGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATag                <  1:4980414/70‑1 (MQ=255)
                                                       aCGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATag                <  1:5685742/70‑1 (MQ=255)
                                                       aCGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATag                <  1:364533/70‑1 (MQ=255)
                                                        cGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATagaa              <  1:464555/71‑1 (MQ=255)
                                                        cGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATagaa              <  1:3890566/71‑1 (MQ=255)
                                                         gCCAGTCGCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCatca                   >  1:1893540/1‑63 (MQ=255)
                                                         gCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATagaag             <  1:1003764/71‑1 (MQ=255)
                                                          ccAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATagaaga            <  1:1625058/71‑1 (MQ=255)
                                                                gCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                                   >  1:3029323/1‑42 (MQ=255)
                                                                gCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                                   >  1:5313032/1‑42 (MQ=255)
                                                                gCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                                   >  1:1142167/1‑42 (MQ=255)
                                                                gCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTc                                   >  1:1026562/1‑42 (MQ=255)
                                                                gCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTg                          >  1:3789575/1‑51 (MQ=255)
                                                                gCCGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGt                         >  1:2675742/1‑52 (MQ=255)
                                                                 ccGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGtt                        >  1:4158798/1‑52 (MQ=255)
                                                                 ccGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCat                     <  1:5532385/55‑1 (MQ=255)
                                                                 ccGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCat                     <  1:4648604/55‑1 (MQ=255)
                                                                  cGTACTCCCGTCAATCGACAGCGCACCAATCAGCACCGTCGGCATATTGTTCATCACTGATGAGAGaaatg    >  1:4332174/1‑69 (MQ=255)
                                                                    tgctgcCATCAATGGACAACGCGCCAACCAGTACCGTCgg                                 <  1:3779870/40‑1 (MQ=255)
                                                                     |                                                                     
TTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCATCAATGGACAACGCGCCAACCAGTACCGTCGGCATATTGTTCATAATAGAAGAGAGGAAGGCG  >  minE/2595476‑2595614

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