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 311,513 C→T 25.7% V454I (GTA→ATA) ‡ acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,5130CT25.7% 212.0 / 62.1 105V454I (GTA→ATA) ‡acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base C (37/41);  new base T (9/18);  total (46/59)
Fisher's exact test for biased strand distribution p-value = 2.62e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.71e-01

Only 100 of 112 total aligned reads displayed.

GCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGG  >  minE/311443‑311581
                                                                      |                                                                    
gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                      >  1:2425457/1‑71 (MQ=255)
gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                      >  1:5294934/1‑71 (MQ=255)
gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                      >  1:5204418/1‑71 (MQ=255)
gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                      >  1:1691408/1‑71 (MQ=255)
 cTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTAc                                                                      <  1:4707146/70‑1 (MQ=255)
 cTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                     <  1:4232480/71‑1 (MQ=255)
   gAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGaa                                                                   >  1:4973337/1‑71 (MQ=255)
    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                     <  1:771359/68‑1 (MQ=255)
    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                     <  1:744121/68‑1 (MQ=255)
    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                     <  1:4191929/68‑1 (MQ=255)
    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                     <  1:4185394/68‑1 (MQ=255)
    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                                     <  1:5077240/68‑1 (MQ=255)
       cAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAcc                                                               <  1:45062/71‑1 (MQ=255)
         aTGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAccgc                                                             >  1:4106045/1‑71 (MQ=255)
          tGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATAccgct                                                            <  1:4585766/71‑2 (MQ=9)
          tGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATAccgct                                                            <  1:4220291/71‑2 (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                                                  <  1:1460261/71‑1 (MQ=255)
                    gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                  <  1:3284158/71‑1 (MQ=255)
                    gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                                  <  1:4286376/71‑1 (MQ=255)
                     aaCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt                                                 <  1:3447088/71‑1 (MQ=9)
                      aCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt                                                 <  1:2281518/70‑1 (MQ=9)
                      aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATc                                                <  1:567990/71‑1 (MQ=255)
                       cTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcg                                               >  1:3512703/1‑71 (MQ=255)
                          gcGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                            <  1:2261693/70‑1 (MQ=12)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                    <  1:4104221/63‑1 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                    <  1:4097488/63‑1 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                    <  1:13856/63‑1 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                    <  1:2462337/63‑1 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                             <  1:61448/70‑1 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgcg                                             <  1:372901/70‑1 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcgc                                              <  1:4589323/69‑1 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                            >  1:3048474/1‑71 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                            >  1:3423818/1‑71 (MQ=255)
                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                                            >  1:2999704/1‑71 (MQ=255)
                            gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGAt                                           <  1:5466771/70‑1 (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)
                                        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                             >  1:254290/1‑71 (MQ=255)
                                         aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                             >  1:5664523/1‑71 (MQ=255)
                                          gTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGcc                            >  1:5383800/1‑71 (MQ=12)
                                          gTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGcc                            >  1:786918/1‑71 (MQ=255)
                                           tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                                <  1:5592764/50‑1 (MQ=9)
                                           tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                                <  1:1082062/50‑1 (MQ=9)
                                           tAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATc                                                <  1:3242049/50‑1 (MQ=9)
                                           tAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa                                          >  1:1141017/1‑56 (MQ=255)
                                           tAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGccc                           >  1:2052512/1‑71 (MQ=255)
                                            aGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCt                          >  1:1240559/1‑71 (MQ=255)
                                            aGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                          >  1:780975/1‑71 (MQ=255)
                                             gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                            >  1:1058364/1‑52 (MQ=9)
                                             gAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGa                                            >  1:817718/1‑52 (MQ=9)
                                             gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAc                                                    <  1:2898020/44‑1 (MQ=255)
                                             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)
                                                  gCCAAAGAAGGCCATCGGTACGAATACCGCGGACAGTACCATCGCGATACCGACCaga                                 >  1:3391834/1‑58 (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)
                                                      aagaagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATAcc                                        <  1:2467516/47‑1 (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)
                                                           ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCg           <  1:5272128/71‑1 (MQ=255)
                                                            gCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                        <  1:905006/57‑1 (MQ=255)
                                                              cATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCTTCGACt        >  1:1866184/1‑71 (MQ=255)
                                                                tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa      >  1:3063381/1‑71 (MQ=255)
                                                                 cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATc                     >  1:5411668/1‑55 (MQ=255)
                                                                  ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg    >  1:4652197/1‑71 (MQ=255)
                                                                  ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCAACTTACg    >  1:5107319/1‑71 (MQ=255)
                                                                    tACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcccc               <  1:3768275/58‑1 (MQ=255)
                                                                    tACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACgg   <  1:3657130/70‑1 (MQ=255)
                                                                     aCGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc     <  1:775211/67‑1 (MQ=255)
                                                                      cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg  >  1:370842/1‑69 (MQ=255)
                                                                      |                                                                    
GCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGG  >  minE/311443‑311581

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