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 311,850 A→T 12.6% V341V (GTT→GTA)  acrB ← multidrug efflux system protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE311,8500AT12.6% 232.6 / 23.0 87V341V (GTT→GTA) acrBmultidrug efflux system protein
Reads supporting (aligned to +/- strand):  ref base A (35/41);  new base T (5/6);  total (40/47)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGAC  >  minE/311780‑311919
                                                                      |                                                                     
tCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTa                                                                       <  1:2852763/71‑1 (MQ=255)
       gAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTa                                                                       <  1:568395/64‑1 (MQ=255)
       gAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACtt                                                                <  1:1908208/71‑1 (MQ=255)
       gAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACtt                                                                >  1:2785062/1‑71 (MQ=255)
       gAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACt                                                                 >  1:243692/1‑70 (MQ=255)
        atattCTGCAAGAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTc                                                               >  1:688874/4‑71 (MQ=16)
        aaGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTc                                                               <  1:2326430/71‑1 (MQ=255)
         aGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCg                                                              <  1:576963/71‑1 (MQ=255)
          gTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGt                                                             <  1:3177601/71‑1 (MQ=255)
           ttCTGCAAGAACAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTg                                                            <  1:2640254/71‑1 (MQ=21)
             cTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAAc                                                                     >  1:2822574/1‑60 (MQ=255)
               gCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTa                                                                       <  1:2295321/56‑1 (MQ=255)
                cAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATa                                                        <  1:2749706/70‑1 (MQ=255)
                cAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCCTGAATa                                                        <  1:912443/70‑1 (MQ=255)
                 aGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATag                                                       <  1:1467086/70‑1 (MQ=255)
                 aGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATag                                                       <  1:41066/70‑1 (MQ=255)
                 aGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATag                                                       <  1:998935/70‑1 (MQ=255)
                  ggAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATa                                                        >  1:3036528/1‑68 (MQ=255)
                   gAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATa                                                        >  1:3152570/1‑67 (MQ=255)
                    aaCATATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATagaaag                                                   >  1:936893/1‑68 (MQ=255)
                    aaCAGATACATCACCAGGAACACCAGCATAATGGCTTCGAACAGCGTTTTTACCACTTCGTGAATagaaag                                                   >  1:2180403/1‑68 (MQ=18)
                     aCAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTa                                                                       <  1:665536/50‑1 (MQ=255)
                      cAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAttt                                                 <  1:2916420/71‑1 (MQ=255)
                       aGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtttt                                                <  1:2519929/71‑1 (MQ=255)
                       aGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtttt                                                >  1:2720296/1‑71 (MQ=255)
                        gATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtttt                                                <  1:2376201/70‑1 (MQ=255)
                        gATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTc                                               <  1:16216/71‑1 (MQ=255)
                         aTACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTc                                                               >  1:1030851/1‑54 (MQ=255)
                         aTACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCa                                              >  1:2419244/1‑71 (MQ=255)
                            cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAAc                                                                     <  1:1544294/45‑1 (MQ=255)
                            cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACg                                            >  1:3619781/1‑70 (MQ=255)
                            cATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACg                                            >  1:3199439/1‑70 (MQ=255)
                             aTAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGaa                                          <  1:458249/71‑1 (MQ=255)
                              tAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACg                                            <  1:1422026/68‑1 (MQ=255)
                               aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACg                                        >  1:3135286/1‑71 (MQ=255)
                               aaCCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACg                                        >  1:3267093/1‑71 (MQ=255)
                                 ccAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGc                                      <  1:1785394/71‑1 (MQ=255)
                                  cAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACggag                                     <  1:1311492/71‑3 (MQ=255)
                                  cAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCg                                     >  1:1722786/1‑71 (MQ=255)
                                   aGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgt                                    <  1:1272663/71‑1 (MQ=255)
                                   aGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgt                                    <  1:553765/71‑1 (MQ=255)
                                    ggAACACGAGGATGATCGCTTCGACCAGCGTTTTAAcc                                                                    <  1:2593737/38‑1 (MQ=255)
                                    ggAACACGAGGATGATCGCTTCGACCAGCGTTTTAAc                                                                     >  1:1449251/1‑37 (MQ=255)
                                    ggAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtg                                   <  1:1604772/71‑1 (MQ=255)
                                    ggAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtg                                   <  1:1442507/71‑1 (MQ=255)
                                      aaCACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtggt                                 <  1:2208850/71‑1 (MQ=255)
                                        cacGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtggt                                 <  1:2805917/69‑1 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACgg                                       >  1:392723/1‑61 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCg                             <  1:1542576/71‑1 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCg                             >  1:1150993/1‑71 (MQ=255)
                                          cGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCg                             >  1:1162280/1‑71 (MQ=255)
                                           gAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGt                            <  1:2697793/71‑1 (MQ=255)
                                           gAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGt                            <  1:1905565/71‑1 (MQ=255)
                                            aGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTa                           >  1:2392995/1‑71 (MQ=255)
                                            aGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTa                           <  1:2057586/71‑1 (MQ=255)
                                            aGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTa                           >  1:1894549/1‑71 (MQ=255)
                                            aGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTa                           <  1:2483885/71‑1 (MQ=255)
                                             ggATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCa                                              >  1:2842723/1‑51 (MQ=255)
                                             ggATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTAt                          <  1:3598567/71‑1 (MQ=255)
                                             ggATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTAt                          >  1:1509933/1‑71 (MQ=255)
                                             ggATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTAt                          >  1:609365/1‑71 (MQ=255)
                                             ggATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAAAGGCGTGGTGTCGTAt                          >  1:3645292/1‑71 (MQ=255)
                                              gatgatCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATg                         <  1:3214708/71‑1 (MQ=255)
                                                  atggCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATa                           >  1:3762878/4‑65 (MQ=255)
                                                  atCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGt                      <  1:1875796/70‑1 (MQ=255)
                                                  atCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTa                     <  1:2937811/71‑1 (MQ=255)
                                                   tCGCTTCGACCAGCGTTTTAACCACTTCGTGAATagag                                                     >  1:158440/1‑38 (MQ=255)
                                                   tCGCTTCGACCAGCGTTTTAACCACTTCGTGAATagag                                                     >  1:795887/1‑38 (MQ=255)
                                                   tCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTa                     <  1:85513/70‑1 (MQ=255)
                                                     gCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAAc                  <  1:2808217/71‑1 (MQ=255)
                                                     gCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAGGGTagag                  <  1:1033738/71‑4 (MQ=16)
                                                     gCTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAGGGTaga                   <  1:2746405/70‑3 (MQ=255)
                                                      cTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAGGGt                      <  1:2505299/66‑1 (MQ=255)
                                                      cTTCGAACAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAGGGTa                     <  1:3251511/67‑1 (MQ=16)
                                                       ttCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtg                                   <  1:2039181/52‑1 (MQ=255)
                                                        tCGACCAGCGTTTTAACCACTTCGTGAATAGAGAtt                                                  >  1:586921/1‑36 (MQ=255)
                                                        tCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCgtggt                                 >  1:1157676/1‑53 (MQ=255)
                                                        tCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGt                            >  1:2126767/1‑58 (MQ=255)
                                                         cGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACaa                <  1:1509709/69‑1 (MQ=255)
                                                         cGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACaa                <  1:1306529/69‑1 (MQ=255)
                                                          gACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAttt             <  1:1820918/71‑1 (MQ=255)
                                                            ccAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTc           <  1:806699/71‑1 (MQ=255)
                                                            acAGCGTTTTTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAgg                        <  1:2884987/57‑1 (MQ=12)
                                                              aGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAAtttt            >  1:1361903/1‑68 (MQ=255)
                                                               gCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGa        >  1:3029372/1‑71 (MQ=255)
                                                                cGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGAc       >  1:2309036/1‑71 (MQ=255)
                                                                 gTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCa          >  1:1919865/1‑67 (MQ=255)
                                                                  ttttTACCACTTCGTGAATAGAAAGCTGGACGAATGGCGTGGTGTCATAAgg                        >  1:2817605/1‑52 (MQ=255)
                                                                    ttAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATggg                       >  1:2337074/1‑51 (MQ=255)
                                                                    ttAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGa        >  1:3565858/1‑66 (MQ=255)
                                                                    ttAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGa   >  1:3821041/1‑71 (MQ=255)
                                                                      aaCCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGAc  <  1:266319/70‑1 (MQ=255)
                                                                      |                                                                     
TCGCGCGGAAGTTCTGCAGGAACAGATACATAACCAGGAACACGAGGATGATCGCTTCGACCAGCGTTTTAACCACTTCGTGAATAGAGATTTTCACGAACGGCGTGGTGTCGTATGGGTAAACAATTTTCAGACCCGAC  >  minE/311780‑311919

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