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 311,544 G→C 28.2% V443V (GTC→GTG)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,5440GC28.2% 124.7 / 50.6 78V443V (GTC→GTG) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (33/23);  new base C (11/11);  total (44/34)
Fisher's exact test for biased strand distribution p-value = 6.13e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCA  >  minE/311475‑311614
                                                                     |                                                                      
gatagCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGa                                                                       >  1:2544643/1‑71 (MQ=255)
   agCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGAc                                                                      >  1:2910826/1‑69 (MQ=255)
    gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                                                    <  1:1459092/70‑1 (MQ=255)
    gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                                                    <  1:4451474/70‑1 (MQ=255)
        cAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTgc                                                                >  1:186789/1‑70 (MQ=12)
        cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                                                                 >  1:3760587/1‑69 (MQ=255)
         aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                                                              >  1:5664523/1‑71 (MQ=255)
         aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc                                                              >  1:254290/1‑71 (MQ=255)
         aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGAAAGTACCATCGCGATACCGACCAGAgcgc                                                              >  1:3427005/1‑71 (MQ=255)
          gTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGcc                                                             >  1:5383800/1‑71 (MQ=12)
          gTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGcc                                                             >  1:786918/1‑71 (MQ=255)
           tAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGccc                                                            >  1:2052512/1‑71 (MQ=255)
            aGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCt                                                           >  1:1240559/1‑71 (MQ=255)
            aGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                                                           >  1:780975/1‑71 (MQ=255)
             gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt                                                           >  1:1090433/1‑70 (MQ=255)
              aaCCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTg                                                          >  1:5073295/1‑70 (MQ=9)
               aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                                                         <  1:718203/70‑1 (MQ=255)
               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)
                     aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcc                                                  >  1:1816424/1‑71 (MQ=255)
                         aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGAcc                                                                     >  1:4923411/1‑48 (MQ=255)
                         aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                                                                    >  1:4654972/1‑49 (MQ=255)
                         aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTg                                                    <  1:3090746/65‑1 (MQ=255)
                           tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg                                            <  1:4761962/70‑1 (MQ=255)
                           tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg                                            <  1:2156899/70‑1 (MQ=255)
                           tgCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCg                                            <  1:457399/70‑1 (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)
                               aTCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt                                         >  1:1423079/1‑70 (MQ=255)
                                tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa                                       >  1:3063381/1‑71 (MQ=255)
                                 cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATc                                                      >  1:4732004/1‑55 (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)
                                        aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGATTTTGcga                                                 >  1:3464653/1‑51 (MQ=19)
                                        aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                                           >  1:5636199/1‑59 (MQ=255)
                                        aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                                           >  1:1861955/1‑59 (MQ=255)
                                        aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                                           >  1:4848865/1‑59 (MQ=255)
                                        aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                                           >  1:3216126/1‑59 (MQ=255)
                                        aaTACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGa                                           >  1:3019711/1‑59 (MQ=255)
                                         aTACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt                                         <  1:3574320/60‑1 (MQ=255)
                                         aTACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt                                         <  1:4281949/60‑1 (MQ=255)
                                          tACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                                     <  1:4381134/47‑1 (MQ=255)
                                          tACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                                     <  1:2928484/47‑1 (MQ=255)
                                           aCCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGAttt                                        <  1:3507797/59‑1 (MQ=255)
                                           aCCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGAttt                                        <  1:1629952/59‑1 (MQ=255)
                                           aCCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc                            >  1:433074/1‑71 (MQ=255)
                                           aCCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc                            >  1:1685943/1‑71 (MQ=255)
                                            ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGc                                                   >  1:2158641/1‑47 (MQ=255)
                                            ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttct                           >  1:1320568/1‑71 (MQ=255)
                                                 gACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                                     <  1:4342965/40‑1 (MQ=255)
                                                   cAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc                            >  1:3349190/1‑63 (MQ=255)
                                                    aGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggcgg                   >  1:246316/1‑71 (MQ=255)
                                                     gcaCCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGATTTTTCCGTCGCTTCTTTTggc                     <  1:4178348/66‑1 (MQ=255)
                                                       aCCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGATTTTTCCGTCGCTTCTTTTggcgggag                >  1:2750095/1‑68 (MQ=255)
                                                        ccATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGAc                                          >  1:5577918/1‑44 (MQ=255)
                                                        ccATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGATTTTTCCGTCGCTTCttt                         <  1:714095/61‑1 (MQ=255)
                                                         cATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATc                                             <  1:3814667/40‑1 (MQ=16)
                                                         cATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGatt                                         <  1:4122318/44‑3 (MQ=16)
                                                         cATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGatt                                         <  1:2529745/44‑3 (MQ=16)
                                                          aTCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCaa                <  1:3859758/68‑1 (MQ=255)
                                                          aTCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAAcc             <  1:1911963/71‑1 (MQ=255)
                                                           tCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACt                                         <  1:2434777/42‑1 (MQ=255)
                                                             gcgATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa                                       >  1:1941244/1‑42 (MQ=255)
                                                             gcgATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACcttc          >  1:914193/1‑71 (MQ=255)
                                                              cgATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg                                     <  1:2847855/43‑1 (MQ=255)
                                                                  aCCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg                                     <  1:1161061/39‑1 (MQ=255)
                                                                  aCCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg                                     <  1:799649/39‑1 (MQ=255)
                                                                   ccGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt                        >  1:5651878/1‑51 (MQ=255)
                                                                   ccGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt                        >  1:4673531/1‑51 (MQ=255)
                                                                     gACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCa  >  1:954246/1‑71 (MQ=255)
                                                                     |                                                                      
GATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCAAACCTTCTTCCGCCA  >  minE/311475‑311614

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