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 311,502 G→T 14.8% A457A (GCC→GCA)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,5020GT14.8% 221.8 / 16.5 74A457A (GCC→GCA) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base G (31/32);  new base T (6/5);  total (37/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.81e-01

GCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCG  >  minE/311435‑311572
                                                                   |                                                                      
gcgcCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGc                                                                      <  1:3260098/70‑1 (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                                                                <  1:1450810/71‑1 (MQ=255)
     aTTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg                                                                <  1:3003775/71‑1 (MQ=255)
      ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg                                                                >  1:414223/1‑70 (MQ=255)
      ttGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCgg                                                                >  1:3866116/1‑70 (MQ=255)
       tGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTa                                                              >  1:3122340/1‑71 (MQ=255)
       tGCCGAAACGATGGTGATAGAGAACTGGCGATAAATTGCCCCAGTAGAACCGCCGAAGAATGCCGTCggaa                                                              >  1:3936622/1‑69 (MQ=9)
            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)
               cAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATAcc                                                      >  1:2666186/1‑71 (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)
                        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)
                              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                          <  1:3768237/70‑1 (MQ=255)
                                            gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                          <  1:3471492/70‑1 (MQ=255)
                                            gCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCa                          <  1:2442503/70‑1 (MQ=255)
                                             ccccAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCagt                        >  1:3500801/3‑70 (MQ=255)
                                             cACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGaa                                                          <  1:105259/37‑1 (MQ=255)
                                             cACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCaga                        <  1:136443/71‑1 (MQ=255)
                                              aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                              <  1:2882105/48‑1 (MQ=255)
                                              aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAg                                              <  1:664219/48‑1 (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)
                                                            cgaagaatGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATa                                 >  1:250651/3‑47 (MQ=16)
                                                            cgaagaatGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGc         >  1:2403519/3‑71 (MQ=255)
                                                            cAAAGAAGGCCATCGGTACGAATACCGCCGACACTACCATCGCGATACCGACCAGAGCGCCCTGa               >  1:2256322/1‑65 (MQ=255)
                                                             aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCAt                                        >  1:2674628/1‑39 (MQ=255)
                                                             aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCAt                                        >  1:1177553/1‑39 (MQ=255)
                                                             aaaGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcc        >  1:403912/1‑71 (MQ=255)
                                                              aagaatGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATAccca                             >  1:228887/1‑47 (MQ=16)
                                                              aagaagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGccc       >  1:1450726/1‑71 (MQ=255)
                                                               agaagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTg                >  1:2517569/1‑61 (MQ=255)
                                                                 aagGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCAt    >  1:3391678/1‑71 (MQ=255)
                                                                   ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGaa              >  1:2542684/1‑59 (MQ=255)
                                                                   ggCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCg  <  1:2045518/71‑1 (MQ=255)
                                                                   |                                                                      
GCGCCATTGCTGAAACAATGGTAATAGAGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCG  >  minE/311435‑311572

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