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 1,014,974 A→G 25.2% R365R (CGT→CGC)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,014,9740AG25.2% 156.3 / 55.1 95R365R (CGT→CGC) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base A (23/48);  new base G (11/13);  total (34/61)
Fisher's exact test for biased strand distribution p-value = 3.25e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TCGTGCCGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAT  >  minE/1014904‑1015037
                                                                      |                                                               
tCGTGCCGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGa                                                                 >  1:4508695/1‑71 (MQ=255)
   tGCCGGTGAGCGACAAACGAGTGGATACCGGGTATTGCGAAAGCTGGGCGAGGATCTCTTTCATCGGGCg                                                               >  1:4963361/1‑70 (MQ=255)
     ccGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGtt                                                            <  1:3604627/71‑1 (MQ=255)
     ccGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGtt                                                            <  1:876619/71‑1 (MQ=255)
     ccGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGtt                                                            <  1:3337592/71‑1 (MQ=255)
      cGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGttt                                                           <  1:30886/71‑2 (MQ=255)
      cGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTa                                                           <  1:3792735/71‑1 (MQ=255)
      cGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTa                                                           <  1:5377619/71‑1 (MQ=255)
      cGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTa                                                           <  1:1923949/71‑1 (MQ=255)
       gTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTaa                                                          <  1:1318515/71‑1 (MQ=255)
       gTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTaa                                                          <  1:5584027/71‑1 (MQ=255)
        ttAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAg                                                         >  1:932552/1‑71 (MQ=255)
          aaGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGt                                                       >  1:4422320/1‑71 (MQ=255)
           aGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTc                                                      <  1:1479785/71‑1 (MQ=255)
           aGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTc                                                      <  1:2106476/71‑1 (MQ=255)
           aGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTc                                                      <  1:5274508/71‑1 (MQ=255)
            gCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCa                                                     <  1:3796929/71‑1 (MQ=255)
            gCGACAAACGAGTGGATACCGGGTATTGCGAAAGCTGGGCGAGGATCTCTTTCATCGGGCGGTTAAGGTCa                                                     <  1:3093759/71‑1 (MQ=255)
             cGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCaa                                                    <  1:163267/71‑1 (MQ=255)
              gATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAAc                                                   <  1:5200294/71‑1 (MQ=255)
               aTAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAAcg                                                  <  1:2166107/71‑1 (MQ=255)
               aTAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAAcg                                                  <  1:4589979/71‑1 (MQ=255)
               aTAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGCTCAAcg                                                  <  1:6717/71‑1 (MQ=255)
               aTAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTACATCGGACGGTTAAGGTCAAcg                                                  <  1:5308426/71‑1 (MQ=255)
                tAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAAcgc                                                 <  1:2421370/71‑1 (MQ=255)
                tAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAAc                                                   >  1:2453114/1‑69 (MQ=255)
                 aaGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAAcgcg                                                >  1:5622352/1‑71 (MQ=255)
                  aGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACgcgc                                               <  1:700668/71‑1 (MQ=255)
                      tgtAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCg                                           <  1:5153970/71‑1 (MQ=255)
                        tAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCt                                         <  1:5422825/71‑1 (MQ=255)
                        tAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCt                                         <  1:734071/71‑1 (MQ=255)
                          gAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTc                                       <  1:4334335/71‑1 (MQ=255)
                          gAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTc                                       <  1:1180063/71‑1 (MQ=255)
                          gAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTc                                       <  1:3522649/71‑1 (MQ=255)
                          gAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTc                                       <  1:5587656/71‑1 (MQ=255)
                           aaaCGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCg                                      <  1:1062587/71‑1 (MQ=255)
                            aaCGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCg                                      <  1:3743063/70‑1 (MQ=255)
                            aaCGGGATACTGCGACAACTGTGCGA‑GATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGcc                                    <  1:5172977/71‑1 (MQ=255)
                             aCGGGATACTGTGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGcc                                    <  1:1118155/71‑1 (MQ=255)
                             aCGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCa                                                     >  1:3647560/1‑54 (MQ=255)
                             aCGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGcc                                    >  1:5463478/1‑71 (MQ=255)
                                 gATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTtct                                >  1:3546580/1‑71 (MQ=255)
                                   tACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACg                                                               >  1:1055246/1‑38 (MQ=255)
                                   tACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACg                                                               >  1:2859702/1‑38 (MQ=255)
                                    attGCGAAAGCTGGGCGAGGATCTCTTTCATCGGGCGGTTaa                                                          >  1:4395814/3‑42 (MQ=21)
                                     ttGCGAAAGCTGGGCGAGGATCTCTTTCATCGGGCGGTTAAGTTCAACTTTCACCGCTTCGCCTTCAccgg                            <  1:987450/70‑3 (MQ=255)
                                     ttGCGAAAGCTGGGCGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTtc                                 <  1:325874/65‑1 (MQ=255)
                                     cTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGc                                     >  1:1841169/1‑62 (MQ=255)
                                       gCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTa                                                           >  1:5266934/1‑38 (MQ=255)
                                       gCGAAAGCTGGGCGAGGATCTCTTTCATCGGGCGGTTAAg                                                         >  1:1590382/1‑40 (MQ=25)
                                       gCGAAAGCTGGGCGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGcc                          >  1:3862539/1‑70 (MQ=255)
                                        cGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCtt                         <  1:62822/71‑1 (MQ=255)
                                          aCAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGc                           <  1:3567322/67‑1 (MQ=255)
                                           cAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgc                      >  1:1127810/1‑71 (MQ=255)
                                            aaCTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCAc                                             >  1:1600901/1‑47 (MQ=255)
                                            aaCTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgcg                     <  1:2852920/71‑1 (MQ=255)
                                             gcTGGGCGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGgcgc                    <  1:4029525/70‑1 (MQ=255)
                                             gcTGGGCGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGgcgc                    <  1:3847078/70‑1 (MQ=255)
                                              cTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGc                                     >  1:3945951/1‑53 (MQ=255)
                                              cTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgcg                     >  1:5190752/1‑69 (MQ=255)
                                              cTGGGCGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCa                   <  1:5281155/71‑1 (MQ=255)
                                               tgtgCGAGGATCTCTTTCATCGGACGGTTAAGGTc                                                      <  1:4018839/35‑1 (MQ=255)
                                               tgtgCGAGGATCTCTTTCATCGGACGGTTAAGGTc                                                      <  1:2386675/35‑1 (MQ=255)
                                               tgtgCGAGGATCTCTTTCATCGGACGGTTAAGGTc                                                      <  1:768274/35‑1 (MQ=255)
                                               tgtgCGAGGATCTCTTTCATCGGACGGTTAAGGTCAAcgc                                                 <  1:3961353/40‑1 (MQ=255)
                                                 tgCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                >  1:2447807/1‑71 (MQ=255)
                                                 tgCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGc                 <  1:4014522/70‑1 (MQ=255)
                                                   cGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttct              <  1:5311474/71‑1 (MQ=255)
                                                    gAGGATCTCTTTCATCGGGCGGTTAATGTCAACTTTCACCGCTTCGcc                                    <  1:4268016/48‑1 (MQ=25)
                                                    gAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGcc                                    <  1:3374172/48‑1 (MQ=37)
                                                    gAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCtt             >  1:4719536/1‑71 (MQ=255)
                                                    gAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCtt             <  1:2465297/71‑1 (MQ=255)
                                                      ggATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTcc           <  1:3887002/71‑1 (MQ=255)
                                                       gATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCttgtg          <  1:4259137/71‑4 (MQ=255)
                                                       gATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCttgtg          <  1:3068296/71‑4 (MQ=255)
                                                         tctcTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttct              >  1:2940352/1‑65 (MQ=255)
                                                         tctcTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttct              >  1:2350452/1‑65 (MQ=255)
                                                           tctTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTtc                                 <  1:5614804/44‑1 (MQ=25)
                                                           tctTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAg                  >  1:5496678/1‑59 (MQ=255)
                                                           tctTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAg                  >  1:4678574/1‑59 (MQ=255)
                                                           tctTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTc                                       <  1:627218/38‑1 (MQ=255)
                                                            ctTTCATCGGGCGGTTAAGGTCAACTTTCACCGCtt                                        >  1:1172061/1‑36 (MQ=19)
                                                             tttCATCGGACGGTTAAGGTCAACGCGCACCTCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCgg         <  1:2311441/66‑1 (MQ=255)
                                                             tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCtt                                  >  1:3832311/1‑41 (MQ=255)
                                                             tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCtt                                  >  1:3682484/1‑41 (MQ=255)
                                                             tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCtt                         <  1:4439401/50‑1 (MQ=255)
                                                             tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCgg         <  1:3736445/66‑1 (MQ=255)
                                                             tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCgg         <  1:1159007/66‑1 (MQ=255)
                                                             tttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGata     >  1:4984110/1‑70 (MQ=255)
                                                              ttCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatata   >  1:2253598/1‑71 (MQ=255)
                                                               tCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTtctc                               >  1:3161498/1‑42 (MQ=255)
                                                               tCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTtctc                               >  1:716215/1‑42 (MQ=255)
                                                               tCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTtctc                               >  1:2481659/1‑42 (MQ=255)
                                                               tCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatat    <  1:580646/69‑1 (MQ=255)
                                                                cATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGatatat  <  1:5345646/70‑1 (MQ=255)
                                                                 aTCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGttc               >  1:191617/1‑56 (MQ=255)
                                                                      |                                                               
TCGTGCCGTTAAGCGATAAGCGTGTAGAAACGGGATACTGCGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAT  >  minE/1014904‑1015037

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