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 311,496 A→G 13.1% F459F (TTT→TTC)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,4960AG13.1% 224.0 / 20.4 84F459F (TTT→TTC) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (33/40);  new base G (6/5);  total (39/45)
Fisher's exact test for biased strand distribution p-value = 7.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCC  >  minE/311427‑311566
                                                                     |                                                                      
tACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCa                                                                        >  1:117680/1‑70 (MQ=255)
 aCCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCa                                                                        >  1:2159153/1‑69 (MQ=255)
 aCCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCa                                                                        >  1:2570316/1‑69 (MQ=255)
  ccGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag                                                                     <  1:1279674/71‑1 (MQ=255)
   cGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga                                                                    <  1:454905/71‑1 (MQ=255)
   cGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga                                                                    <  1:1460748/71‑1 (MQ=255)
   cGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga                                                                    <  1:1799279/71‑1 (MQ=255)
    gACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa                                                                   <  1:3497770/71‑1 (MQ=255)
        gcgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGc                                                                <  1:3260098/70‑1 (MQ=255)
         cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa                                                                   >  1:2682644/1‑66 (MQ=255)
         cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa                                                                   >  1:1819940/1‑66 (MQ=255)
         cgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCa                                                              <  1:2867743/71‑1 (MQ=255)
          gcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCAt                                                             <  1:3408709/71‑1 (MQ=255)
          gcCATTGCCGAAACGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCAt                                                             <  1:2113064/71‑1 (MQ=9)
            cATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCg                                                           >  1:2119889/1‑71 (MQ=255)
             aTTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg                                                          <  1:3003775/71‑1 (MQ=255)
             aTTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg                                                          <  1:1450810/71‑1 (MQ=255)
              ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg                                                          >  1:3866116/1‑70 (MQ=255)
              ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg                                                          >  1:414223/1‑70 (MQ=255)
               tGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa                                                        >  1:3122340/1‑71 (MQ=255)
               tGCCGAAACGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCGTCggaa                                                        >  1:3936622/1‑69 (MQ=9)
                gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag                                                                     <  1:1593080/57‑1 (MQ=255)
                gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag                                                                     <  1:556139/57‑1 (MQ=255)
                gCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaag                                                                     <  1:2815359/57‑1 (MQ=255)
                    aaaCGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCAt                                                             >  1:2092038/1‑61 (MQ=9)
                    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACg                                                      <  1:2689047/68‑1 (MQ=255)
                    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGaa                                                    >  1:574802/1‑70 (MQ=255)
                    aaaCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAAt                                                   <  1:3545284/71‑1 (MQ=255)
                      aCAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaaga                                                                    >  1:2491536/1‑52 (MQ=255)
                       cAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAcc                                                >  1:2666186/1‑71 (MQ=255)
                         aTGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAaagaa                                                                   >  1:3392439/1‑50 (MQ=255)
                          tGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAccgcc                                             >  1:48657/1‑71 (MQ=255)
                             tAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa                                           >  1:3192846/1‑70 (MQ=255)
                             tAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa                                           >  1:2841052/1‑70 (MQ=255)
                             tAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGa                                           >  1:702752/1‑70 (MQ=255)
                               aTAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCgaa                                                                      >  1:422278/1‑41 (MQ=12)
                                tAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa                                                        >  1:410310/1‑54 (MQ=255)
                                   agaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATa                                                  >  1:348051/1‑57 (MQ=255)
                                   agaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAcc                                    <  1:2784490/71‑1 (MQ=255)
                                    gaACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCa                                   >  1:960071/1‑71 (MQ=255)
                                     aaCTGGCGATAAATTGCCCCAGTAGAACCGCCgaagaa                                                                   >  1:2747381/1‑38 (MQ=12)
                                     aaCTGACGATAGATAGCACCAGTAGAACCGCCAaagaa                                                                   >  1:3022234/1‑38 (MQ=255)
                                      aCTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCAt                                  <  1:880954/70‑1 (MQ=9)
                                      aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCAt                                  <  1:2531350/70‑1 (MQ=255)
                                      aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATc                                 <  1:2104716/71‑1 (MQ=255)
                                      aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATc                                 <  1:3754158/71‑1 (MQ=255)
                                      aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCAGCGGTACGAATACCGCCGACAGTACCATc                                 <  1:1121581/71‑1 (MQ=255)
                                       atGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcg                                >  1:1725338/2‑71 (MQ=255)
                                        tGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATcg                                >  1:2672090/1‑70 (MQ=255)
                                        tGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGAACCAt                                  <  1:1535646/68‑1 (MQ=255)
                                          aCGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGa                             >  1:1412848/1‑71 (MQ=255)
                                            gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa                           <  1:1264754/71‑1 (MQ=255)
                                            gatagataGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa                           >  1:2727115/1‑71 (MQ=255)
                                              tagatagCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAccgcc                                             <  1:443508/51‑1 (MQ=255)
                                              tagatagCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATAcc                         <  1:812398/71‑1 (MQ=255)
                                                    gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCag                   <  1:3266831/71‑1 (MQ=255)
                                                    gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCag                   <  1:177690/71‑1 (MQ=255)
                                                    gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                    <  1:2442503/70‑1 (MQ=255)
                                                    gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                    <  1:3768237/70‑1 (MQ=255)
                                                    gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                    <  1:3471492/70‑1 (MQ=255)
                                                     ccccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCagt                  >  1:3500801/3‑70 (MQ=255)
                                                     cACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGaa                                                    <  1:105259/37‑1 (MQ=255)
                                                     cACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCaga                  <  1:136443/71‑1 (MQ=255)
                                                      aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                        <  1:664219/48‑1 (MQ=255)
                                                      aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                        <  1:2882105/48‑1 (MQ=255)
                                                      aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                        <  1:266734/48‑1 (MQ=255)
                                                      aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                 <  1:2957357/71‑1 (MQ=255)
                                                      aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                 <  1:3841463/71‑1 (MQ=255)
                                                        cAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATAc                          >  1:1743140/1‑60 (MQ=18)
                                                        cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAccgc                                              >  1:3775808/1‑40 (MQ=255)
                                                        cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCaga                  >  1:2827285/1‑68 (MQ=255)
                                                        cAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTAACATCGCGATACCGACCAGAgc                >  1:3517937/1‑70 (MQ=255)
                                                         aGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCAc                                     <  1:3759833/48‑1 (MQ=12)
                                                         aGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTgcg               >  1:3705393/1‑70 (MQ=255)
                                                         aGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAgcgc              >  1:556739/1‑71 (MQ=255)
                                                          gTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGcc             >  1:2353725/1‑71 (MQ=255)
                                                           tAGAGCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGt                                       >  1:2681797/1‑44 (MQ=255)
                                                           tAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGAt                            <  1:1074038/55‑1 (MQ=255)
                                                             gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt           >  1:3370656/1‑70 (MQ=255)
                                                             gAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCt           >  1:3637324/1‑70 (MQ=255)
                                                              aaCCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGa         <  1:3401176/71‑1 (MQ=255)
                                                               aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATa                           <  1:1926786/52‑1 (MQ=255)
                                                               aCCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGaa        >  1:2304363/1‑71 (MQ=255)
                                                                 cGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAAtt      <  1:3165198/71‑2 (MQ=255)
                                                                 cGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                    >  1:1067930/1‑57 (MQ=255)
                                                                  gCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAAttt     >  1:3818268/1‑69 (MQ=255)
                                                                  gCCAAAGAAGGCCATCGGTACTAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt     <  1:3610260/71‑1 (MQ=255)
                                                                  gCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt     <  1:2487857/71‑1 (MQ=255)
                                                                    cAAAGAAGGCCATCGGTACGAATACCGCCGACACTACCATCGCGATACCGACCAGAGCGCCCTGa         >  1:2256322/1‑65 (MQ=255)
                                                                     aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCAt                                  >  1:1177553/1‑39 (MQ=255)
                                                                     aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCAt                                  >  1:2674628/1‑39 (MQ=255)
                                                                     aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcc  >  1:403912/1‑71 (MQ=255)
                                                                     |                                                                      
TACCGACAGCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCC  >  minE/311427‑311566

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