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 2,636,243 G→A 26.3% intergenic (+63/‑35) ugpB → / → ugpA glycerol‑3‑phosphate transporter subunit/glycerol‑3‑phosphate transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,636,2430GA26.3% 120.2 / 44.8 76intergenic (+63/‑35)ugpB/ugpAglycerol‑3‑phosphate transporter subunit/glycerol‑3‑phosphate transporter subunit
Reads supporting (aligned to +/- strand):  ref base G (29/27);  new base A (10/10);  total (39/37)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.56e-01

TCTTAATCAGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTCGCGCTGG  >  minE/2636175‑2636313
                                                                    |                                                                      
tCTTAATCAGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATaagcgaa                                                                      <  1:5006102/71‑1 (MQ=255)
 aacgcctgatgcgacgctggcgcgtcttatcaggcctacacgctgcgatttTGTAGGCCGGATaagcaaag                                                                     >  1:2528465‑M2/52‑71 (MQ=255)
  ttAATCAGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATaagcgaagc                                                                    >  1:1437845/1‑71 (MQ=255)
  acgcctgatgcgacgctgacgcgtcttatctggcctacacgctgcgatttTGTAGGCCGGATaagcaaag                                                                     <  1:1266928‑M2/20‑1 (MQ=255)
    gcctgatgcgacgctggcgcgtcttatcaggcctacgcgctgcgatttTGTAGGCCGGATAAGCAAAgcgc                                                                  <  1:270646‑M2/23‑1 (MQ=255)
    gcctgatgcgacgctggcgcgtcttatcaggcctacacgctgcgatttTGTAGGCCGGATaagcaaagcg                                                                   >  1:5269286‑M2/49‑70 (MQ=255)
    gcctgatgcgacgctgacgcgtcttatctggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAgcgc                                                                  <  1:4307580‑M2/23‑1 (MQ=255)
    aaTCAGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATaagcgaagc                                                                    <  1:589441/69‑1 (MQ=255)
    aaTCAGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATaagcgaagc                                                                    <  1:1382265/69‑1 (MQ=255)
     cctgatgcgacgctggcgcgtcttatcaggcctacgcgctgcgatttTGTAGGCCGGATAAGCAAAGCGCa                                                                 <  1:1028253‑M2/24‑1 (MQ=255)
      ctgatgcgacgctggcgcgtcttatcaggcctacgcgctgcgatttTGTAGGCCGGATAAGCAAAGCGCa                                                                 <  1:3871861‑M2/24‑1 (MQ=255)
       tgatgcgacgctggcgcgtcttatcaggcctacgcgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATc                                                               >  1:4757524‑M2/46‑71 (MQ=255)
        gatgcgacgctgacgcgtcttatctggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCa                                                                 >  1:3802728‑M2/45‑68 (MQ=255)
        aGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATcc                                                              >  1:3674514/1‑71 (MQ=255)
          tgtAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCgg                                                            <  1:3359110/71‑1 (MQ=255)
          tgtAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCgg                                                            <  1:3580218/71‑1 (MQ=255)
          tgtAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCgg                                                            <  1:2067953/71‑1 (MQ=255)
           gcgacgctggcgcgtcttatcaggcctacgcgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCgg                                                            >  1:1124834‑M2/42‑70 (MQ=255)
            cgacgctgacgcgtcttatctggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCGGca                                                          >  1:5385333‑M2/41‑71 (MQ=255)
             gacgctggcgcgtcttatcaggcctacgcgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCGgcat                                                         <  1:3170691‑M2/32‑2 (MQ=255)
             gacgctggcgcgtcttatcaggcctacgcgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCGgcat                                                         <  1:3128084‑M2/32‑2 (MQ=255)
               tGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATaagcgaagcg                                                                   <  1:2086068/59‑1 (MQ=255)
               tGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAg                                                       >  1:1106203/1‑71 (MQ=255)
                gctggcgcgtcttatcaggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCGgcacg                                                        >  1:781071‑M2/37‑68 (MQ=255)
                 tCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGtt                                                     >  1:4350278/1‑71 (MQ=255)
                 tCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGt                                                      >  1:1105735/1‑70 (MQ=255)
                 ctggcgcgtcttatcaggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCGgcacg                                                        <  1:4337157‑M2/33‑2 (MQ=255)
                   ggATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGtt                                                     >  1:477951/1‑69 (MQ=255)
                      tGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAgg                                                 >  1:1533721/1‑70 (MQ=255)
                      tGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAgg                                                 >  1:4407920/1‑70 (MQ=255)
                      tGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAgg                                                 >  1:78835/1‑70 (MQ=255)
                       gCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAgg                                                 <  1:2126782/69‑1 (MQ=255)
                       gCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAgg                                                 <  1:41093/69‑1 (MQ=255)
                         tcttatctggcctacacgctgcgatttTGTAGGCCGGATAAGTAAAGCGCATCCgg                                                            <  1:239818‑M2/29‑1 (MQ=255)
                           ttatcaggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCcggcacgaa                                                      >  1:3667330‑M2/26‑57 (MQ=255)
                           ttatcaggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCcggcacgaa                                                      >  1:275120‑M2/26‑57 (MQ=255)
                           ttatcaggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCcggcacgaa                                                      >  1:3674019‑M2/26‑57 (MQ=255)
                           ttCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTaa                                           >  1:2248718/1‑71 (MQ=255)
                            tCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATaagcgaa                                                                      <  1:3986098/43‑1 (MQ=255)
                             atctggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCgg                                                            >  1:3957820‑M2/24‑52 (MQ=255)
                             atctggcctacacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCgg                                                            >  1:182445‑M2/24‑52 (MQ=255)
                              gCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAAtt                                             <  1:1877587/66‑1 (MQ=255)
                               cTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGt                                       <  1:2769740/71‑1 (MQ=255)
                                ttATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGt                                       >  1:1940197/1‑70 (MQ=255)
                                   tCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAAt                                    <  1:2887788/70‑1 (MQ=255)
                                       cacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCgg                                                            <  1:3349995‑M2/29‑1 (MQ=255)
                                       cacgctgcgatttTGTAGGCCGGATAAGCAAAGCGCATCCgg                                                            <  1:5572349‑M2/29‑1 (MQ=255)
                                       aCCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtcat                               <  1:2122513/71‑1 (MQ=255)
                                       aCCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtca                                <  1:5439324/70‑1 (MQ=255)
                                        ccTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtcatc                              <  1:2187801/71‑1 (MQ=255)
                                         cTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtcatca                             >  1:1918414/1‑71 (MQ=255)
                                            gCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTcatcat                            <  1:287537/69‑1 (MQ=255)
                                            gCATCGCGTATAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTcatcat                            <  1:3120013/69‑1 (MQ=255)
                                               tCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTa                                      <  1:113643/56‑1 (MQ=255)
                                                 gcgTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTATTGTCATCATCCCGTcc                     >  1:2552987/1‑71 (MQ=255)
                                                 gcgTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtcat                               >  1:4562886/1‑61 (MQ=255)
                                                 gcgTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATccc                         >  1:5169364/1‑67 (MQ=255)
                                                 gcgTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTcc                     >  1:4201742/1‑71 (MQ=255)
                                                 gcgTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTc                      <  1:884715/70‑1 (MQ=255)
                                                 gcgTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTc                      <  1:2791723/70‑1 (MQ=255)
                                                   gtgtAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTaa                                     >  1:23604/1‑53 (MQ=255)
                                                    tgtAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtcat                               <  1:1748185/58‑1 (MQ=255)
                                                         gCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCatcatc                           <  1:3779586/57‑1 (MQ=255)
                                                         gCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCatcatc                           <  1:4767240/57‑1 (MQ=255)
                                                         gCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCatcatc                           <  1:2571221/57‑1 (MQ=255)
                                                         gCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTcc             >  1:2861230/1‑71 (MQ=255)
                                                         gCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTcc             >  1:5472103/1‑71 (MQ=255)
                                                          ccGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCg            >  1:1307498/1‑71 (MQ=255)
                                                          ccGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCg            >  1:3961788/1‑71 (MQ=255)
                                                          ccGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCg            >  1:1231063/1‑71 (MQ=255)
                                                          ccGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCg            >  1:2332703/1‑71 (MQ=255)
                                                          ccGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCg            >  1:4673509/1‑71 (MQ=255)
                                                           cGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGc           <  1:3455796/71‑1 (MQ=255)
                                                            ggATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCt          >  1:3950934/1‑71 (MQ=255)
                                                            ggATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCt          >  1:1425137/1‑71 (MQ=255)
                                                             gATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTa                                            <  1:1812644/36‑1 (MQ=255)
                                                             gATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTa                                            <  1:758817/36‑1 (MQ=255)
                                                             gATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACTGTAATGTCATCATCCCGTCCGATGTTCCGCTc         >  1:3878947/1‑71 (MQ=255)
                                                             gATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCg                        <  1:1309590/56‑1 (MQ=255)
                                                             gATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGt                       <  1:2610774/57‑1 (MQ=255)
                                                              aTAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtc                                 >  1:1805740/1‑46 (MQ=255)
                                                               tAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtcatca                             >  1:551115/1‑49 (MQ=255)
                                                               tAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGtcatc                              <  1:4075349/48‑1 (MQ=255)
                                                               tAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTcgc       <  1:3736780/71‑1 (MQ=255)
                                                               tAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTcgc       >  1:72039/1‑71 (MQ=255)
                                                                aagcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTcgcg      >  1:1056407/1‑71 (MQ=255)
                                                                 agcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATg                                   <  1:5182803/41‑1 (MQ=255)
                                                                 agcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCt          >  1:93095/1‑66 (MQ=255)
                                                                 agcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTcgcg      <  1:129852/70‑1 (MQ=255)
                                                                 agcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTCgcgc     <  1:592819/71‑1 (MQ=255)
                                                                  gcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCgg                   <  1:3754738/56‑1 (MQ=255)
                                                                  gcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCgg                   <  1:3373374/56‑1 (MQ=255)
                                                                  gcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCgg                   <  1:2467415/56‑1 (MQ=255)
                                                                  gcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCgg                   <  1:1733476/56‑1 (MQ=255)
                                                                  gcgaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCgg                   <  1:960122/56‑1 (MQ=255)
                                                                    gaagcgCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTCGCgctgg  >  1:1851128/1‑71 (MQ=255)
                                                                    |                                                                      
TCTTAATCAGTGTAATGTCGGATGCGTTTCGCTTATCTGACCTGGCATCGCGTGTAGGCCGGATAAGCGAAGCGCATCCGGCACAGTTCAGGAATTAACCGTAATGTCATCATCCCGTCCGGTGTTCCGCTCGCGCTGG  >  minE/2636175‑2636313

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