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 F21 I0 R1 2169 63.0 3952800 76.2% 3012033 62.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,595,485 C→T 21.5% L371L (TTG→TTA)  arsB ← arsenite/antimonite transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,595,4850CT21.5% 236.3 / 58.4 116L371L (TTG→TTA) arsBarsenite/antimonite transporter
Reads supporting (aligned to +/- strand):  ref base C (42/49);  new base T (15/10);  total (57/59)
Fisher's exact test for biased strand distribution p-value = 2.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.48e-01

Only 100 of 121 total aligned reads displayed.

ATTCTTCTGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAT  >  minE/2595416‑2595552
                                                                     |                                                                   
atTCTTCTGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTccc                                                                     >  1:769487/1‑70 (MQ=255)
 ttcttcTGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCaa                                                                   <  1:2313497/71‑1 (MQ=255)
   cttctGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCaaa                                                                  <  1:3880676/70‑1 (MQ=255)
    ttctGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATc                                                                >  1:3061286/1‑71 (MQ=255)
      ctGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCg                                                               >  1:2872330/1‑70 (MQ=255)
      ctGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCg                                                               <  1:2438638/70‑1 (MQ=255)
      ctGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCg                                                               <  1:1361854/70‑1 (MQ=255)
          gAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGc                                                           >  1:469164/1‑70 (MQ=255)
          gAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGc                                                           >  1:3683788/1‑70 (MQ=255)
           aaaGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGc                                                           >  1:744154/1‑69 (MQ=255)
           aaaGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGc                                                           >  1:1781988/1‑69 (MQ=255)
            aaGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCaa                                                        >  1:1406051/1‑71 (MQ=255)
              gTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATc                                                      <  1:1687020/71‑1 (MQ=255)
                aCGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATca                                                     >  1:1281937/1‑70 (MQ=255)
                 cGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATcaca                                                   >  1:1926630/1‑71 (MQ=255)
                 cGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATcaca                                                   <  1:3130744/71‑1 (MQ=255)
                  gTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCa                                                                    <  1:114021/53‑1 (MQ=255)
                   tGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACAtt                                                 <  1:2537102/71‑1 (MQ=255)
                    gaaGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTg                                                >  1:3682967/3‑71 (MQ=255)
                    gCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTg                                                >  1:1279832/1‑71 (MQ=255)
                    gCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTg                                                >  1:328935/1‑71 (MQ=255)
                    gCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTg                                                >  1:3045573/1‑71 (MQ=255)
                    gCAGCCACAGCAGAGTTGCCAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTg                                                >  1:3239388/1‑71 (MQ=255)
                     cAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTg                                                <  1:1043247/70‑1 (MQ=255)
                     cAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTg                                                <  1:831074/70‑1 (MQ=255)
                      aGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTg                                                <  1:2735754/69‑1 (MQ=255)
                        ccAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCa                                             >  1:2097381/1‑70 (MQ=255)
                         cAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATa                                           <  1:3680750/71‑1 (MQ=255)
                          agagTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATa                                           >  1:927278/1‑70 (MQ=255)
                           gagTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATcaca                                                   <  1:2372881/61‑1 (MQ=255)
                           gagTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACAtt                                                 >  1:875123/1‑63 (MQ=255)
                            agTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAc                                        >  1:65735/1‑71 (MQ=255)
                             gtagcgtagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAcc                                       <  1:2796306/71‑1 (MQ=255)
                              tagcgtagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCa                                      <  1:1573024/71‑1 (MQ=255)
                               agcgtagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCa                                      <  1:1378962/70‑1 (MQ=255)
                               agcgtagcCAGGCTACCAATTGGGGTAATTTTAGGTCCCAAATc                                                                >  1:43043/1‑44 (MQ=255)
                                gcgtagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATca                                                     <  1:2354634/54‑1 (MQ=255)
                                gcgtagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATc                                    >  1:2131489/1‑71 (MQ=255)
                                 cgtagcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATc                                                      <  1:300475/52‑1 (MQ=255)
                                     gcCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGcc                                                          <  1:807950/44‑1 (MQ=255)
                                     gcCAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCAtt                                    <  1:3134047/66‑2 (MQ=255)
                                       cAGACTGCCAATCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGcctctt                             <  1:3613558/71‑1 (MQ=255)
                                        aGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCg                                                               <  1:2198133/36‑1 (MQ=255)
                                           cTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGa                          >  1:3749195/1‑70 (MQ=255)
                                            tACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGAt                         >  1:1270227/1‑70 (MQ=255)
                                              ccAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATaa                       <  1:3592426/70‑1 (MQ=255)
                                              ccAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATaa                       <  1:496167/70‑1 (MQ=255)
                                              ccAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAAc                      >  1:2744289/1‑71 (MQ=255)
                                              ccAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAAc                      <  1:686166/71‑1 (MQ=255)
                                               cAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACg                     >  1:3597233/1‑71 (MQ=255)
                                                aaTCGGGGTGATTTTCGGGCCTAAATCACAGCCGATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                    >  1:1067913/1‑71 (MQ=255)
                                                aaTCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                    <  1:2056505/71‑1 (MQ=255)
                                                aaTCGGGGTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGc                    >  1:1142962/1‑71 (MQ=255)
                                                 aTTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGcc                   <  1:448498/71‑1 (MQ=255)
                                                 aTTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGc                    >  1:1826369/1‑70 (MQ=255)
                                                  ttGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCa                  <  1:966097/71‑1 (MQ=255)
                                                   cggggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGc                                              >  1:3645109/2‑42 (MQ=25)
                                                   cggggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGc                                              >  1:3469152/2‑42 (MQ=25)
                                                     gggTGATTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAgtc               <  1:1039489/71‑3 (MQ=255)
                                                       gTAATTTTCTGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGc             >  1:3629754/1‑71 (MQ=255)
                                                       gTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATc                                    <  1:45937/48‑1 (MQ=255)
                                                        tAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAAcc                                       <  1:3684269/44‑1 (MQ=255)
                                                        tAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCa                                      <  1:963935/45‑1 (MQ=255)
                                                        tAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGcc            <  1:1716718/71‑1 (MQ=255)
                                                         gaTTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCg           >  1:2310222/2‑71 (MQ=255)
                                                         aaTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCa                                             >  1:920003/1‑37 (MQ=255)
                                                         aaTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCg           >  1:3548375/1‑71 (MQ=255)
                                                          aTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATc                                    >  1:3104766/1‑45 (MQ=255)
                                                          aTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATc                                    >  1:1823567/1‑45 (MQ=255)
                                                          aTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAAGGCCAGATGCCGt          >  1:3657593/1‑71 (MQ=255)
                                                          aTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCg           <  1:3632583/70‑1 (MQ=255)
                                                          aTTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGt          >  1:3045419/1‑71 (MQ=255)
                                                          aTTTTCGGTCCCAAATCGCACCCAATCACATTGGCATAAACCATc                                    >  1:3530414/1‑45 (MQ=255)
                                                          aTTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCttt                            >  1:1575010/1‑53 (MQ=255)
                                                          aTTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAg                 <  1:2776004/64‑1 (MQ=255)
                                                          aTTTTCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAg                 <  1:373726/64‑1 (MQ=255)
                                                           ttttCGGGCCTAAATCACAGCCAATCACATTGGCATaaatc                                       <  1:636744/41‑3 (MQ=255)
                                                            tttCGGTCCCAAATCGCAGCCAATCACATTGGCATaa                                          >  1:152663/1‑37 (MQ=255)
                                                             ttCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgct       >  1:1834918/1‑71 (MQ=255)
                                                              tCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctg      >  1:1079007/1‑71 (MQ=255)
                                                              tCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAg                 >  1:1243003/1‑60 (MQ=255)
                                                              tCGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGtactc      >  1:1335928/1‑70 (MQ=255)
                                                               cGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGcct                                >  1:3654912/1‑42 (MQ=255)
                                                               cGGGCCTAAATCACAGCCAATCACATTGGCATAAATCATTGCCTCTTTGACGACGCCAGTCGCCGtactc      <  1:1014757/70‑2 (MQ=255)
                                                                ggTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctgc     <  1:2603902/70‑1 (MQ=255)
                                                                ggTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctgc     >  1:1098596/1‑70 (MQ=255)
                                                                ggTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGcc    <  1:2138816/71‑1 (MQ=255)
                                                                 gTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCa   <  1:3081292/71‑1 (MQ=255)
                                                                 gTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCa   <  1:3379826/71‑1 (MQ=255)
                                                                  tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTg                           <  1:2384325/46‑1 (MQ=255)
                                                                  tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTg                           <  1:2643761/46‑1 (MQ=255)
                                                                  tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTg                           <  1:803192/46‑1 (MQ=255)
                                                                  tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCat                 <  1:3070565/56‑2 (MQ=255)
                                                                  tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAg                 <  1:2746220/56‑1 (MQ=255)
                                                                  tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtg         <  1:3699881/64‑1 (MQ=255)
                                                                  tCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtg         <  1:1221579/64‑1 (MQ=255)
                                                                   cccAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGtgctg      >  1:3733789/1‑66 (MQ=255)
                                                                   cccAAATCGAAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAt  >  1:556/1‑70 (MQ=255)
                                                                     cAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGAt               >  1:1126735/1‑55 (MQ=255)
                                                                     cAAATCGCAGCCAATCACATTGGCATAAAACATCGCTTCTTTGATaa                       >  1:1108861/1‑47 (MQ=255)
                                                                     |                                                                   
ATTCTTCTGCGAAAGTACGTGCAGCCAGAGTAGCGTAGCCAGGCTACCAATTGGGGTAATTTTCGGTCCCAAATCGCAGCCAATCACATTGGCATAAACCATCGCTTCTTTGATAACGCCAGATGCCGTGCTGCCAT  >  minE/2595416‑2595552

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