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 311,811 A→C 24.2% V354V (GTT→GTG)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,8110AC24.2% 243.0 / 83.2 124V354V (GTT→GTG) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (32/62);  new base C (16/14);  total (48/76)
Fisher's exact test for biased strand distribution p-value = 8.42e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 134 total aligned reads displayed.

CGAGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAAC  >  minE/311741‑311880
                                                                      |                                                                     
cGAGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAcatacata                                                                       <  1:128063/71‑1 (MQ=255)
cGAGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATa                                                                       <  1:2566942/71‑1 (MQ=255)
  aacAACACCACGGGTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCAc                                                                     >  1:4922309/3‑71 (MQ=2)
  aacAACACCACGGGTACCGCAATGGTGGGGATCAGAGTTGCTCGCATATTCTGCAAGAACAGATACATCAc                                                                     >  1:5222363/3‑71 (MQ=2)
  aGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAAc                                                                     <  1:966593/71‑1 (MQ=255)
  aGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAAc                                                                     <  1:2970212/71‑1 (MQ=255)
   gCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAAcc                                                                    <  1:1008852/71‑1 (MQ=255)
   acAACACCACGGGTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCAc                                                                     >  1:1975921/2‑70 (MQ=2)
   acAACACCACGGGTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCAc                                                                     >  1:1661494/2‑70 (MQ=2)
     aacaccacgGGTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAg                                                                  >  1:4596896/4‑71 (MQ=2)
      acaccacgGGTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAgg                                                                 <  1:4670260/69‑1 (MQ=9)
        accacgGGTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAgg                                                                 <  1:1106224/69‑1 (MQ=9)
         ccaccGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGaa                                                               >  1:4377344/1‑70 (MQ=255)
         ccaccGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAac                                                              <  1:403968/71‑1 (MQ=255)
           acgggTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAg                                                                  >  1:3124164/4‑65 (MQ=2)
           acgggTACCGCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAGGAacac                                                            <  1:5493422/68‑1 (MQ=9)
           accGGTACGGCAATGGTCGGAATCAACTTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAacac                                                            <  1:4566776/71‑1 (MQ=255)
           accGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAgg                                                                 <  1:4882378/66‑1 (MQ=255)
           accGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAacac                                                            <  1:297754/71‑1 (MQ=255)
           accGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAacac                                                            <  1:3584368/71‑1 (MQ=255)
                tACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGga                                                       >  1:2878751/1‑71 (MQ=255)
                 aCGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGgat                                                      >  1:4248622/1‑71 (MQ=255)
                  ccgCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAGGAACACCAGcat                                                      <  1:3775086/68‑1 (MQ=9)
                  ccgCAATGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAGGAACACCAGcat                                                      <  1:786931/68‑1 (MQ=9)
                  cGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGgatg                                                     <  1:4147432/71‑1 (MQ=255)
                  cGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGgatg                                                     <  1:109107/71‑1 (MQ=255)
                    gCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGgatgat                                                   <  1:1848565/71‑1 (MQ=255)
                    gCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGgatgat                                                   <  1:5089969/71‑1 (MQ=255)
                      aaTGGTGGGGATCAGCGTTGCTCGCATATTCTGCAAGAACAGATACATCACCAGGACCACCAGcataatg                                                  >  1:5560352/1‑69 (MQ=2)
                      aaTGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATaa                                                                      >  1:2928644/1‑50 (MQ=255)
                        tGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAgg                                                                 <  1:1423131/53‑1 (MQ=255)
                        tGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAg                                                         <  1:3154050/61‑1 (MQ=255)
                        tGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAg                                                         <  1:5267957/61‑1 (MQ=255)
                        tGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAg                                                         <  1:2015780/61‑1 (MQ=255)
                        tGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAg                                                         <  1:1524122/61‑1 (MQ=255)
                         ggTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAg                                                         >  1:4168476/1‑60 (MQ=255)
                         ggTCGGAATCAACGTCGCGAGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCtt                                              >  1:5645169/1‑71 (MQ=255)
                            cGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGa                                           >  1:1014996/1‑71 (MQ=255)
                                aTCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAg                                       >  1:1071591/1‑71 (MQ=255)
                                aTCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAg                                       >  1:2390574/1‑71 (MQ=255)
                                 tCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACg                                                           <  1:1713518/50‑1 (MQ=255)
                                 tCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGgatg                                                     <  1:2094437/56‑1 (MQ=255)
                                     cGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAgg                                                                 <  1:4869205/40‑1 (MQ=255)
                                     cGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGttt                                  >  1:1417996/1‑71 (MQ=255)
                                     cGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGttt                                  >  1:2748303/1‑71 (MQ=255)
                                      gTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGtttt                                 <  1:4208913/71‑1 (MQ=255)
                                      gTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGtttt                                 <  1:3121986/71‑1 (MQ=255)
                                      gTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGtttt                                 <  1:3234591/71‑1 (MQ=255)
                                      gTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGtttt                                 <  1:1484380/71‑1 (MQ=255)
                                      gTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGtttt                                 <  1:950230/71‑1 (MQ=255)
                                       tCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCg                                     <  1:1937636/66‑1 (MQ=255)
                                       tCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTa                                <  1:3918965/71‑1 (MQ=255)
                                       tCGCGCGGAAGTTCTGAAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCg                                     <  1:2248828/66‑1 (MQ=255)
                                         gcgcgGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                               >  1:1197818/1‑70 (MQ=255)
                                         gcgcgGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTaa                               >  1:3370189/1‑70 (MQ=255)
                                            cgGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCAc                           <  1:4399059/71‑1 (MQ=255)
                                             ggAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACt                          >  1:3698759/1‑71 (MQ=255)
                                              gAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAgg                                                        <  1:3898201/40‑1 (MQ=255)
                                                aGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGa                                           >  1:3504734/1‑51 (MQ=255)
                                                  ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCa                                        <  1:4895700/52‑1 (MQ=255)
                                                  ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCa                                        <  1:5266851/52‑1 (MQ=255)
                                                  ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCa                                        <  1:4535045/52‑1 (MQ=255)
                                                  ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTg                     <  1:1448128/71‑1 (MQ=255)
                                                  ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTg                     <  1:5126597/71‑1 (MQ=255)
                                                  ttCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTg                     <  1:1266517/71‑1 (MQ=255)
                                                  ttCTGCAAGAACAGATACATCACCAGGAACACCAGCATAATGGCTTCg                                            >  1:4140710/1‑48 (MQ=12)
                                                  ttCTGCAAGAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGt                      >  1:2819597/1‑70 (MQ=18)
                                                  ttCTGCAAGAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGt                      >  1:4502896/1‑70 (MQ=18)
                                                   tCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTg                     >  1:4024720/1‑70 (MQ=255)
                                                   tCTGCAAGAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTg                     >  1:3099907/1‑70 (MQ=18)
                                                    cTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGc                                      >  1:2516665/1‑52 (MQ=255)
                                                    cTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGaa                   >  1:2686001/1‑71 (MQ=255)
                                                       caagAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGaa                   >  1:716852/4‑68 (MQ=21)
                                                       cAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAAt                  <  1:207952/69‑1 (MQ=255)
                                                         agAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATaga               >  1:224138/2‑70 (MQ=21)
                                                          gAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATagaaa             <  1:4424764/71‑3 (MQ=18)
                                                            aCAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATagaaa             >  1:3916900/1‑67 (MQ=18)
                                                            aCAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCa                            <  1:2979806/54‑1 (MQ=255)
                                                            aCAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtt           >  1:4570445/1‑71 (MQ=255)
                                                            aCAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtt           >  1:4664282/1‑71 (MQ=255)
                                                              aGATACATAACCAGGAACACGAGGATGATCGCTTCGAcc                                         >  1:3670653/1‑39 (MQ=255)
                                                                aTACATCACCAGGAACACCAGCATAATGGCTTCGaa                                          <  1:2625063/36‑2 (MQ=12)
                                                                aTACATCACCAGGAACACCAGCATAATGGCTTCGaa                                          <  1:2692604/36‑2 (MQ=12)
                                                                aTACATCACCAGGAACACCAGCATAATGGCTTCGaa                                          <  1:376063/36‑2 (MQ=12)
                                                                aTACATAACGAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCa       >  1:1882947/1‑71 (MQ=255)
                                                                aTACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGaa                   <  1:1598976/59‑1 (MQ=255)
                                                                  aCATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCAc      >  1:4986943/1‑70 (MQ=255)
                                                                   cATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGttttt                                <  1:412807/43‑2 (MQ=16)
                                                                   cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGa    <  1:4763334/71‑1 (MQ=255)
                                                                   cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGa    <  1:1791893/71‑1 (MQ=255)
                                                                   cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGa    <  1:2122378/71‑1 (MQ=255)
                                                                    aTAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGaa                   >  1:3922039/1‑55 (MQ=255)
                                                                    aTAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCa       >  1:4590069/1‑67 (MQ=255)
                                                                    aTAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTACGTGAATAGAGATTTTCa       >  1:4825532/1‑67 (MQ=255)
                                                                    aTAACCAGGAACACGAGGATGATCCCTTCGACCAGCGTTTTAACCACTTCGTGaa                   >  1:1751603/1‑55 (MQ=255)
                                                                      aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGtttt                                 >  1:620188/1‑39 (MQ=255)
                                                                      aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga               >  1:1121544/1‑57 (MQ=255)
                                                                      aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga               >  1:5133547/1‑57 (MQ=255)
                                                                      aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga               >  1:3212469/1‑57 (MQ=255)
                                                                      aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATaga               >  1:3942716/1‑57 (MQ=255)
                                                                      |                                                                     
CGAGCAATACCACCGGTACGGCAATGGTCGGAATCAACGTCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAAC  >  minE/311741‑311880

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