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 311,529 T→C 16.0% V448V (GTA→GTG)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,5290TC16.0% 203.4 / 27.3 84V448V (GTA→GTG) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base T (34/36);  new base C (8/5);  total (42/42)
Fisher's exact test for biased strand distribution p-value = 5.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.51e-01

AGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCA  >  minE/311462‑311599
                                                                   |                                                                      
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                                                                  <  1:3754158/71‑1 (MQ=255)
   aCTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATc                                                                  <  1:2104716/71‑1 (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)
           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)
                  cACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCaga                                                   <  1:136443/71‑1 (MQ=255)
                   aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                                                  <  1:3841463/71‑1 (MQ=255)
                   aCCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCagag                                                  <  1:2957357/71‑1 (MQ=255)
                     cAGTAGAACCGCCGAAGAATGCCATCGGAATAAATACCGCTGACAGCACCATCGCGATAc                                                           >  1:1743140/1‑60 (MQ=18)
                     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)
                                          ccATCGGAATAAATACCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGat                           >  1:976105/1‑70 (MQ=255)
                                           cATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGa                                          <  1:1269278/55‑1 (MQ=255)
                                             tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                      <  1:1606618/57‑1 (MQ=255)
                                             tCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTa                        >  1:361136/1‑71 (MQ=255)
                                              cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                       >  1:905829/1‑71 (MQ=255)
                                              cGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                       >  1:901156/1‑71 (MQ=255)
                                               ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                       <  1:2640374/70‑1 (MQ=255)
                                               ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTAc                       <  1:2000163/70‑1 (MQ=255)
                                               ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg                      >  1:3086170/1‑71 (MQ=255)
                                               ggTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACg                      >  1:2299603/1‑71 (MQ=255)
                                                 tACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg                    <  1:1733761/71‑1 (MQ=255)
                                                   cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa                            >  1:709963/1‑61 (MQ=255)
                                                   cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACggg                    >  1:3645596/1‑69 (MQ=255)
                                                   cGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGt                   <  1:611625/70‑1 (MQ=255)
                                                    gAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGaa                                         <  1:1139968/47‑1 (MQ=255)
                                                       tACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGctt              <  1:1490520/71‑1 (MQ=255)
                                                        aCCGCTGACAGCACCATCGCGATACCCACCAGTGCGCCCTGAATTTGCGACATCGAttttt                       <  1:3933907/61‑3 (MQ=255)
                                                         ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttct            <  1:3703952/71‑1 (MQ=255)
                                                         ccgccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGcttc             <  1:1845213/70‑1 (MQ=255)
                                                            ccgACAGTACGATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt                         <  1:2372600/55‑1 (MQ=255)
                                                            ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCt                                      <  1:293599/42‑1 (MQ=255)
                                                            ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt         >  1:3561011/1‑71 (MQ=255)
                                                            ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt         >  1:117307/1‑71 (MQ=255)
                                                            ccgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCtttt         >  1:3026723/1‑71 (MQ=255)
                                                             cgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACtt                         <  1:1856760/54‑1 (MQ=255)
                                                             cgACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTg        <  1:1364338/71‑1 (MQ=255)
                                                              gACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACgg                     >  1:209257/1‑57 (MQ=255)
                                                              gACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTgg       <  1:161871/71‑1 (MQ=255)
                                                                  gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGcccc                                 >  1:307287/1‑41 (MQ=255)
                                                                  gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa                            >  1:1192713/1‑46 (MQ=255)
                                                                  gTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGa                            <  1:350186/46‑1 (MQ=255)
                                                                   tACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTggcggc   >  1:2325397/1‑70 (MQ=255)
                                                                   tACCATCGCGATACCGACAAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCa  <  1:2533555/71‑1 (MQ=255)
                                                                   |                                                                      
AGAACTGACGATAGATAGCACCAGTAGAACCGCCAAAGAAGGCCATCGGTACGAATACCGCCGACAGTACCATCGCGATACCGACCAGAGCGCCCTGAATCTGCCCCATCGACTTACGGGTAGCTTCTTTTGGCGGCA  >  minE/311462‑311599

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