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 2,584,314 A→G 22.7% V988A (GTT→GCT)  mdtF ← multidrug transporter, RpoS‑dependent

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,584,3140AG22.7% 248.5 / 62.3 119V988A (GTT→GCT) mdtFmultidrug transporter, RpoS‑dependent
Reads supporting (aligned to +/- strand):  ref base A (47/45);  new base G (11/16);  total (58/61)
Fisher's exact test for biased strand distribution p-value = 3.87e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.60e-01

Only 100 of 121 total aligned reads displayed.

GGCAAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGC  >  minE/2584244‑2584384
                                                                      |                                                                      
ggCAAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATaa                                                                        <  1:3434867/71‑1 (MQ=255)
 gCAAACATCCCACCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAAc                                                                       <  1:1517813/71‑1 (MQ=255)
  cAAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAAc                                                                       <  1:859642/70‑1 (MQ=255)
  cAAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAAc                                                                       >  1:2414109/1‑70 (MQ=255)
  cAAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAAc                                                                       >  1:3157592/1‑70 (MQ=255)
   aaaCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAAc                                                                       >  1:3675681/1‑69 (MQ=255)
   aaaCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAAc                                                                       >  1:2202186/1‑69 (MQ=255)
     aCATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGc                                                                   <  1:2005434/71‑1 (MQ=255)
      cATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGc                                                                   <  1:3667268/70‑1 (MQ=255)
      cATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCg                                                                  >  1:340559/1‑71 (MQ=255)
             cccATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCAc                                                           >  1:2568325/1‑71 (MQ=255)
             cccATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCAc                                                           >  1:3668171/1‑71 (MQ=255)
              ccATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACg                                                          <  1:765931/71‑1 (MQ=255)
                   aCGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        >  1:5471326/1‑68 (MQ=255)
                      ccGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGaa                                                   >  1:531115/1‑70 (MQ=255)
                       cgatacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAAt                                                  >  1:1730401/4‑70 (MQ=9)
                       cgatacccacaGCGTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATa                                                 <  1:2237258/68‑1 (MQ=9)
                       cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                  >  1:1950990/1‑70 (MQ=255)
                       cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                 <  1:2445552/71‑1 (MQ=255)
                       cGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATa                                                 <  1:5205726/71‑1 (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)
                            cctaccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAg                                                                    <  1:5339496/47‑1 (MQ=255)
                               accGCGTTTTGAGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCAc                                                           >  1:384676/1‑53 (MQ=255)
                                ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                          >  1:1625428/1‑69 (MQ=255)
                                ccGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                          >  1:2544561/1‑69 (MQ=255)
                                 cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                       <  1:1895414/71‑1 (MQ=255)
                                 cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagag                                       <  1:4008447/71‑1 (MQ=255)
                                 cgcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGCCAGCACGCCGAGAATAAAGGCCagag                                       <  1:768882/71‑1 (MQ=255)
                                 agcgTTCTGCGCGCCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGcga                                          >  1:4694479/2‑66 (MQ=9)
                                  gcgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATaa                                                >  1:1059270/1‑61 (MQ=255)
                                   cgTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagagag                                     >  1:5291444/1‑71 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        <  1:4764709/50‑1 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        <  1:4760626/50‑1 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGcc                                                        <  1:4521918/50‑1 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGc                                            <  1:4992602/62‑1 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCaga                                        <  1:5564802/66‑1 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCaga                                        <  1:562964/66‑1 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                          <  1:4791385/64‑1 (MQ=255)
                                     ttttGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCa                                          <  1:3214057/64‑1 (MQ=255)
                                        tGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGtcat                                >  1:391086/1‑71 (MQ=255)
                                          cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcatc                               <  1:4469410/70‑1 (MQ=255)
                                          cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcat                                <  1:4289323/69‑1 (MQ=255)
                                          cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcat                                <  1:129252/69‑1 (MQ=255)
                                          cgcgcCACTGCCGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGtcat                                <  1:1735021/69‑1 (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                                        >  1:1120242/2‑52 (MQ=255)
                                                    ccGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACg                    <  1:1165271/71‑1 (MQ=9)
                                                     cGGCACCGTTACTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACg                    >  1:20626/1‑70 (MQ=9)
                                                      ggCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                  <  1:4030879/71‑1 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAAt                                                  <  1:2535918/38‑1 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                      <  1:1835747/50‑1 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                      <  1:4760639/50‑1 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                      <  1:3166582/50‑1 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                      <  1:4724158/50‑1 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCagaga                                      <  1:5239277/50‑1 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                  >  1:3605538/1‑70 (MQ=255)
                                                       gCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTa                  >  1:4600369/1‑70 (MQ=255)
                                                          ccATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                               >  1:2335523/1‑38 (MQ=255)
                                                          ccATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                               >  1:345050/1‑38 (MQ=255)
                                                          ccATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                               >  1:688751/1‑38 (MQ=255)
                                                          ccATGACTGATAACCAGCGGCAGCACGCCGAGAATaaa                                               >  1:4262358/1‑38 (MQ=255)
                                                          ccATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAgg                            <  1:4370925/57‑1 (MQ=255)
                                                          ccATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACg              <  1:3864851/71‑1 (MQ=255)
                                                           cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                           <  1:5678795/57‑1 (MQ=255)
                                                           cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                           <  1:4750877/57‑1 (MQ=255)
                                                           cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGc             <  1:1370591/71‑1 (MQ=255)
                                                           cATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGc             <  1:2464338/71‑1 (MQ=255)
                                                            gttaCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGgacgcagacgca            >  1:5043168/4‑71 (MQ=2)
                                                            gttaCTGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGgacgcagacgca            <  1:544853/68‑1 (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                   <  1:3747188/59‑2 (MQ=9)
                                                                 tGATAGCTAGCGGTAATACGCCGAGAATAAAGGCGAGAGAGGTCATCAGGATAGGACgc                   <  1:1845112/59‑2 (MQ=9)
                                                                   aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGa                           >  1:2473156/1‑49 (MQ=255)
                                                                   aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaaa                >  1:5475533/1‑60 (MQ=255)
                                                                   aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTaa                 >  1:4321275/1‑59 (MQ=255)
                                                                   aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCAt           >  1:3998547/1‑65 (MQ=255)
                                                                   aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCcgcg      >  1:4958936/1‑70 (MQ=255)
                                                                   aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCgcgc     >  1:1885653/1‑71 (MQ=255)
                                                                   aTAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCgcgc     >  1:3171747/1‑71 (MQ=255)
                                                                      aCCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGcgccgc  >  1:377027/1‑71 (MQ=255)
                                                                      |                                                                      
GGCAAACATCCCGCCCATCACGCCGGTACCTACCGCGTTTTGCGCGCCAGAACCGGCACCATGACTGATAACCAGCGGCAGCACGCCGAGAATAAAGGCCAGAGAGGTCATCAGGATTGGGCGTAAACGCATCCGCGCCGC  >  minE/2584244‑2584384

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