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 311,511 T→A 24.1% V454V (GTA→GTT) ‡ acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,5110TA24.1% 246.4 / 71.9 112V454V (GTA→GTT) ‡acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base T (45/40);  new base A (9/18);  total (54/58)
Fisher's exact test for biased strand distribution p-value = 8.26e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.13e-01

Only 100 of 117 total aligned reads displayed.

TTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGG  >  minE/311441‑311580
                                                                      |                                                                     
ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGt                                                                       <  1:64888/71‑1 (MQ=255)
ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGt                                                                       <  1:3403910/71‑1 (MQ=255)
ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGt                                                                       <  1:5332686/71‑1 (MQ=255)
  gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                     >  1:2425457/1‑71 (MQ=255)
  gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                     >  1:1691408/1‑71 (MQ=255)
  gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                     >  1:5204418/1‑71 (MQ=255)
  gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                     >  1:5294934/1‑71 (MQ=255)
   cTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                     <  1:4707146/70‑1 (MQ=255)
   cTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                    <  1:4232480/71‑1 (MQ=255)
      aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                    <  1:4191929/68‑1 (MQ=255)
      aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                    <  1:4185394/68‑1 (MQ=255)
      aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                    <  1:744121/68‑1 (MQ=255)
      aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                    <  1:5077240/68‑1 (MQ=255)
         cAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAcc                                                              <  1:45062/71‑1 (MQ=255)
           aTGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAccgc                                                            >  1:4106045/1‑71 (MQ=255)
            tGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATAccgct                                                           >  1:4012000/1‑70 (MQ=9)
            tGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATAccgct                                                           <  1:4220291/71‑2 (MQ=9)
            tGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATAccgct                                                           <  1:4585766/71‑2 (MQ=9)
            tGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATAccgct                                                           <  1:115177/71‑2 (MQ=9)
              gTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa                                                         <  1:2636719/71‑1 (MQ=255)
                 aTAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGaa                                                                  >  1:3368717/1‑59 (MQ=255)
                 aTAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                                      >  1:4973468/1‑71 (MQ=255)
                 aTAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                                      >  1:5367023/1‑71 (MQ=255)
                  tAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACa                                                       <  1:679377/69‑1 (MQ=255)
                   agagAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa                                                         <  1:788602/66‑1 (MQ=255)
                   agagAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTa                                                    >  1:1350901/1‑71 (MQ=255)
                    gagaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                     >  1:5282410/1‑53 (MQ=255)
                      gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                 <  1:2545083/71‑1 (MQ=255)
                      gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                 <  1:3284158/71‑1 (MQ=255)
                       aaCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt                                                <  1:3447088/71‑1 (MQ=9)
                        aCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt                                                <  1:2281518/70‑1 (MQ=9)
                        aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa                                                                      <  1:1229471/48‑1 (MQ=255)
                         cTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcg                                              >  1:3512703/1‑71 (MQ=255)
                            gcGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                           <  1:2261693/70‑1 (MQ=12)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                   <  1:4097488/63‑1 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                   <  1:2462337/63‑1 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                   <  1:13856/63‑1 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                            <  1:61448/70‑1 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                            <  1:372901/70‑1 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgc                                             <  1:4589323/69‑1 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                           >  1:2999704/1‑71 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                           >  1:3048474/1‑71 (MQ=255)
                            aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                           >  1:3423818/1‑71 (MQ=255)
                              gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa                                                                      >  1:2097921/1‑42 (MQ=255)
                              gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa                                                                      >  1:2907225/1‑42 (MQ=255)
                              gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa                                                                      >  1:3021514/1‑42 (MQ=255)
                              gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGAt                                          <  1:5466771/70‑1 (MQ=255)
                              gataaattGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATa                                         <  1:4363444/71‑1 (MQ=255)
                                  gatagCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGa                                     >  1:2544643/1‑71 (MQ=255)
                                     agCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGAc                                    >  1:2910826/1‑69 (MQ=255)
                                      gccccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATa                                         >  1:3179630/4‑63 (MQ=12)
                                      gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                  <  1:1459092/70‑1 (MQ=255)
                                      gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                  <  1:4451474/70‑1 (MQ=255)
                                        cccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCAcc                                                  <  1:1448029/51‑1 (MQ=12)
                                        cccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCAcc                                                  <  1:5367771/51‑1 (MQ=12)
                                          cAGTAGAACCGCCGAAGAATGCCATCGGAATAAATAccgct                                                           <  1:5424972/41‑2 (MQ=9)
                                          cAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTgc                              >  1:186789/1‑70 (MQ=12)
                                          cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                               >  1:3760587/1‑69 (MQ=255)
                                           aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                 >  1:3184393/1‑50 (MQ=255)
                                           aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                 >  1:4201841/1‑50 (MQ=255)
                                           aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                            >  1:5664523/1‑71 (MQ=255)
                                           aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                            >  1:254290/1‑71 (MQ=255)
                                           aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGAAAGTACCATCGCGATACCGACCAGAgcgc                            >  1:3427005/1‑71 (MQ=255)
                                            gTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGcc                           >  1:786918/1‑71 (MQ=255)
                                             tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                               <  1:1082062/50‑1 (MQ=9)
                                             tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                               <  1:5592764/50‑1 (MQ=9)
                                             tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                               <  1:3242049/50‑1 (MQ=9)
                                             tAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa                                         >  1:1141017/1‑56 (MQ=255)
                                              aGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                         >  1:780975/1‑71 (MQ=255)
                                               gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                           >  1:5134930/1‑52 (MQ=9)
                                               gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                           >  1:1058364/1‑52 (MQ=9)
                                               gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                           >  1:817718/1‑52 (MQ=9)
                                               gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                            >  1:1799234/1‑51 (MQ=255)
                                               gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                         >  1:1090433/1‑70 (MQ=255)
                                                aaCCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTg                        >  1:5073295/1‑70 (MQ=9)
                                                 aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                       <  1:260009/70‑1 (MQ=255)
                                                 aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                       <  1:718203/70‑1 (MQ=255)
                                                    gCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                   <  1:2642158/71‑1 (MQ=255)
                                                      cgaagaatGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGc                 <  1:593814/69‑1 (MQ=255)
                                                       aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                            >  1:5360285/1‑43 (MQ=255)
                                                       aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcc                >  1:1816424/1‑71 (MQ=255)
                                                        aagaagGCCATCGGTACGAATACCGCCGACAGTACCa                                                 <  1:3429659/37‑1 (MQ=255)
                                                         agaagGCCATCGGTACGAATACCGCCGACAGTACCATcgc                                             <  1:1871110/40‑1 (MQ=255)
                                                           aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                           >  1:3224752/1‑40 (MQ=255)
                                                           aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGAcc                                   >  1:4923411/1‑48 (MQ=255)
                                                           aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                  >  1:4654972/1‑49 (MQ=255)
                                                            agGCCATCGGTACGAATACCGCCGACAGTACCATcgc                                             <  1:4894642/37‑1 (MQ=255)
                                                            agGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATAcc                                       <  1:1399055/43‑1 (MQ=255)
                                                             tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg          <  1:457399/70‑1 (MQ=255)
                                                             tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg          <  1:2156899/70‑1 (MQ=255)
                                                             tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg          <  1:4761962/70‑1 (MQ=255)
                                                             ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCg          <  1:5518337/71‑1 (MQ=255)
                                                              gCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                       <  1:905006/57‑1 (MQ=255)
                                                                cATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCTTCGACt       >  1:1866184/1‑71 (MQ=255)
                                                                 aTCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt       >  1:1423079/1‑70 (MQ=255)
                                                                  tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa     >  1:3063381/1‑71 (MQ=255)
                                                                   cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATc                    >  1:5411668/1‑55 (MQ=255)
                                                                   cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATc                    >  1:4732004/1‑55 (MQ=255)
                                                                    ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCAACTTACg   >  1:5107319/1‑71 (MQ=255)
                                                                      tACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcccc              <  1:3768275/58‑1 (MQ=255)
                                                                      |                                                                     
TTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGG  >  minE/311441‑311580

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A