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 2,584,324 G→A 23.5% L985L (CTG→TTG) ‡ mdtF ← multidrug transporter, RpoS‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,584,3240GA23.5% 243.4 / 60.6 115L985L (CTG→TTG) ‡mdtFmultidrug transporter, RpoS‑dependent
Reads supporting (aligned to +/- strand):  ref base G (44/44);  new base A (11/16);  total (55/60)
Fisher's exact test for biased strand distribution p-value = 5.10e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.39e-01

Only 100 of 118 total aligned reads displayed.

CCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCGATG  >  minE/2584257‑2584391
                                                                   |                                                                   
 ccATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACg                                                                 <  1:765931/71‑1 (MQ=255)
  cATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGc                                                                >  1:5622025/1‑71 (MQ=255)
      aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                               >  1:5471326/1‑68 (MQ=255)
         ccGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGaa                                                          >  1:1165698/1‑70 (MQ=255)
          cgatacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAAt                                                         >  1:1730401/4‑70 (MQ=9)
          cgatacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATa                                                        <  1:2237258/68‑1 (MQ=9)
          cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                         >  1:1950990/1‑70 (MQ=255)
          cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                        <  1:5205726/71‑1 (MQ=255)
          cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                        <  1:2445552/71‑1 (MQ=255)
            gTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                                      <  1:1516042/71‑1 (MQ=255)
            gTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                        >  1:2285179/1‑69 (MQ=255)
            atacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATaaa                                                      <  1:4123503/70‑1 (MQ=9)
            atacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATaaa                                                      <  1:852092/70‑1 (MQ=9)
             tacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAg                                                     <  1:4715207/71‑1 (MQ=9)
                  accGCGTTTTGAGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCAc                                                                  >  1:384676/1‑53 (MQ=255)
                   ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                                 >  1:1625428/1‑69 (MQ=255)
                   ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                                 >  1:2544561/1‑69 (MQ=255)
                    cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                              <  1:4008447/71‑1 (MQ=255)
                    cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                              <  1:1895414/71‑1 (MQ=255)
                    cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGCCAGCACGCCGAGAATAAAGGCCagag                                              <  1:768882/71‑1 (MQ=255)
                    agcgTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGcga                                                 >  1:4694479/2‑66 (MQ=9)
                     gcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                       >  1:3908394/1‑61 (MQ=255)
                     gcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                       >  1:1059270/1‑61 (MQ=255)
                     gcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                       >  1:5171755/1‑61 (MQ=255)
                      cgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagagag                                            >  1:5291444/1‑71 (MQ=255)
                       gTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCaga                                               <  1:4306235/67‑1 (MQ=255)
                        ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                               <  1:4521918/50‑1 (MQ=255)
                        ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                               <  1:4760626/50‑1 (MQ=255)
                        ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                               <  1:4764709/50‑1 (MQ=255)
                        ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCaga                                               <  1:562964/66‑1 (MQ=255)
                        ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                                 <  1:3214057/64‑1 (MQ=255)
                        ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                                 <  1:4791385/64‑1 (MQ=255)
                           tGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtcat                                       >  1:391086/1‑71 (MQ=255)
                            gcgcgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtcat                                       <  1:3554749/70‑1 (MQ=255)
                             cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcatc                                      <  1:4469410/70‑1 (MQ=255)
                             cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcat                                       <  1:4900481/69‑1 (MQ=255)
                             cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcat                                       <  1:129252/69‑1 (MQ=255)
                             cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcat                                       <  1:1735021/69‑1 (MQ=255)
                             cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcat                                       <  1:4289323/69‑1 (MQ=255)
                             cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGgcat                                       <  1:4282731/69‑1 (MQ=255)
                               cgcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                                   <  1:3756472/71‑1 (MQ=255)
                                gcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                                  >  1:503638/1‑71 (MQ=255)
                                gcCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                                  >  1:5537871/1‑71 (MQ=255)
                                 ccAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAt                                 <  1:162097/71‑1 (MQ=255)
                                  cAGAACCGGCACCATGACTGATAACCAGAGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGAtt                                >  1:365942/1‑71 (MQ=255)
                                     tgccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGAt                                 <  1:4171865/65‑1 (MQ=12)
                                      gccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCgaga                                               >  1:4517874/2‑52 (MQ=255)
                                      gccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCgaga                                               >  1:2230835/2‑52 (MQ=255)
                                      gccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCgaga                                               >  1:1120242/2‑52 (MQ=255)
                                       ccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACg                           <  1:1165271/71‑1 (MQ=9)
                                       ccGGCAACGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACg                           >  1:735007/1‑71 (MQ=9)
                                         ggCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                         <  1:4758177/71‑1 (MQ=255)
                                         ggCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                         <  1:5418138/71‑1 (MQ=255)
                                         ggCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                         <  1:4030879/71‑1 (MQ=255)
                                         ggCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                         <  1:245938/71‑1 (MQ=255)
                                          gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                         <  1:2535918/38‑1 (MQ=255)
                                          gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                             <  1:4724158/50‑1 (MQ=255)
                                          gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                             <  1:3166582/50‑1 (MQ=255)
                                          gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                             <  1:5239277/50‑1 (MQ=255)
                                          gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                             <  1:1835747/50‑1 (MQ=255)
                                          gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                         >  1:3605538/1‑70 (MQ=255)
                                             ccATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                                      >  1:4262358/1‑38 (MQ=255)
                                             ccATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                                      >  1:345050/1‑38 (MQ=255)
                                             ccATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagtgag                                            <  1:2822000/48‑1 (MQ=255)
                                             ccATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                                   <  1:3692448/57‑1 (MQ=255)
                                             ccATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                                   <  1:4370925/57‑1 (MQ=255)
                                              cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                                   <  1:4535269/56‑1 (MQ=255)
                                              cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                                  <  1:4750877/57‑1 (MQ=255)
                                              cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                                  <  1:5678795/57‑1 (MQ=255)
                                              cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGc                    <  1:1370591/71‑1 (MQ=255)
                                              cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGc                    <  1:2464338/71‑1 (MQ=255)
                                               gttaCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGgacgcagacgca                   <  1:544853/68‑1 (MQ=2)
                                               gttaCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGgacgcagacgca                   >  1:5043168/4‑71 (MQ=2)
                                               aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                             >  1:1880683/1‑45 (MQ=255)
                                               aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                                 >  1:1698327/1‑41 (MQ=255)
                                               aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGt                                          >  1:3468221/1‑48 (MQ=255)
                                               aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                                   >  1:66371/1‑55 (MQ=255)
                                               aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTg                               >  1:4813082/1‑59 (MQ=255)
                                               aTGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGACAGGTCATCAGGATTGGGCGTaa                        >  1:1121840/1‑66 (MQ=255)
                                                ttaCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACGCAGACg                     >  1:1321823/3‑68 (MQ=9)
                                                 taCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGa                                  >  1:2929012/2‑54 (MQ=17)
                                                  aCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGt                                          >  1:1137416/1‑45 (MQ=16)
                                                   cTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACGCAGACGCATAcg               <  1:602202/71‑1 (MQ=9)
                                                    tGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACgc                          <  1:1845112/59‑2 (MQ=9)
                                                    tGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACgc                          <  1:3747188/59‑2 (MQ=9)
                                                      aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                                  >  1:2473156/1‑49 (MQ=255)
                                                      aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaaa                       >  1:5475533/1‑60 (MQ=255)
                                                      aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCAt                  >  1:3998547/1‑65 (MQ=255)
                                                      aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCcgcg             >  1:4958936/1‑70 (MQ=255)
                                                      aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCgcgc            >  1:3171747/1‑71 (MQ=255)
                                                      aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCgcgc            >  1:1885653/1‑71 (MQ=255)
                                                         aCCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGcgccgc         >  1:377027/1‑71 (MQ=255)
                                                          ccAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCt        <  1:5679229/71‑1 (MQ=255)
                                                          ccAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCt        <  1:3438055/71‑1 (MQ=255)
                                                            aGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTc      <  1:1230076/71‑1 (MQ=255)
                                                               ggCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCgat   <  1:2225644/71‑1 (MQ=255)
                                                               ggCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCg     >  1:2095808/1‑69 (MQ=255)
                                                                gcagcaCGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCgatg  <  1:126222/71‑1 (MQ=255)
                                                                gcagcaCGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCgatg  <  1:4232838/71‑1 (MQ=255)
                                                                gcagcaCGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCgatg  <  1:774471/71‑1 (MQ=255)
                                                                   |                                                                   
CCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGCTTCGATG  >  minE/2584257‑2584391

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