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 1,015,163 G→A 43.9% R302R (CGC→CGT)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,1630GA43.9% 50.4 / 131.6 114R302R (CGC→CGT) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base G (25/39);  new base A (20/30);  total (45/69)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.12e-01

Only 100 of 120 total aligned reads displayed.

GATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCG  >  minE/1015097‑1015230
                                                                  |                                                                   
gATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGa                                                                  <  1:5118496/70‑1 (MQ=255)
 atatTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAAt                                                                >  1:5249545/1‑71 (MQ=255)
   atTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCa                                                              >  1:4396330/1‑71 (MQ=255)
    ttACGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAAc                                                             >  1:4556881/1‑71 (MQ=255)
      aCGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCAcgc                                                           >  1:4825718/1‑71 (MQ=255)
       cGGTCAGCGGAGCAGGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAAcgcg                                                          <  1:4992893/71‑1 (MQ=255)
        ggTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCAcgc                                                           <  1:124909/69‑1 (MQ=255)
        ggTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCgg                                                         <  1:5372228/71‑1 (MQ=255)
            agcggagcagGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGt                                                     >  1:5579161/1‑71 (MQ=255)
            agcagagcagGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATg                                                      <  1:4931657/70‑1 (MQ=255)
              cagagcagGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCg                                                   <  1:3972203/71‑1 (MQ=255)
               ggagcagGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCg                                                   <  1:4468816/69‑1 (MQ=255)
               ggagcagGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGt                                                  <  1:1066112/70‑1 (MQ=255)
               agagcagGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCg                                                   <  1:1080131/70‑1 (MQ=255)
                 agcagGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAAcgcg                                                          <  1:2555907/61‑1 (MQ=255)
                   cagGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGc                                              <  1:44878/71‑1 (MQ=255)
                    agGAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGcgcg                                             <  1:1667475/71‑1 (MQ=255)
                     ggAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGcgcg                                             >  1:5622372/1‑70 (MQ=255)
                     ggAGACGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGa                                            <  1:4194267/71‑1 (MQ=255)
                       agaCGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAg                                          <  1:3884826/71‑1 (MQ=255)
                       agaCGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAg                                          <  1:550342/71‑1 (MQ=255)
                       agaCGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAg                                          <  1:2178286/71‑1 (MQ=255)
                        gaCGCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAg                                          >  1:3118423/1‑70 (MQ=255)
                          cGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTAt                                       >  1:515647/1‑71 (MQ=255)
                           gCCCATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTAtt                                      <  1:2853639/71‑1 (MQ=255)
                            cccATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTgcgc                                              <  1:2705980/62‑1 (MQ=255)
                            cccATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTgcgc                                              <  1:2241003/62‑1 (MQ=255)
                             ccATGCCGACCGGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTa                                    <  1:3622182/71‑1 (MQ=255)
                              cATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTac                                   >  1:1605888/1‑71 (MQ=255)
                               atgccgaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTacc                                  <  1:5183224/68‑1 (MQ=255)
                               aTACCGACCGGGCAGTATGCGCCGTGACGTGGCAGGCGAAt                                                                <  1:4568092/41‑1 (MQ=255)
                               aTACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAAt                                                                <  1:1732405/41‑1 (MQ=255)
                               aTACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAAt                                                                <  1:4156888/41‑1 (MQ=255)
                               aTACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAAt                                                                <  1:1725854/41‑1 (MQ=255)
                               aTACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAAt                                                                <  1:3047222/41‑1 (MQ=255)
                                tACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTa                                        <  1:1456498/64‑1 (MQ=255)
                                tACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTAttt                                     <  1:5133979/67‑1 (MQ=255)
                                tACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTAttt                                     <  1:2331947/67‑1 (MQ=255)
                                tACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTacca                                 >  1:761644/1‑71 (MQ=255)
                                tACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTacca                                 >  1:5632792/1‑71 (MQ=255)
                                tACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTacca                                 >  1:3721887/1‑71 (MQ=255)
                                  ccgaccgGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTAtt                                      >  1:3575939/1‑64 (MQ=255)
                                  ccgaccgGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTac                                   <  1:5179/67‑1 (MQ=255)
                                  ccgaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGt                                                     >  1:3366147/1‑49 (MQ=255)
                                  ccgaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGt                                                     >  1:825820/1‑49 (MQ=255)
                                  ccgaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGt                                                     >  1:4965512/1‑49 (MQ=255)
                                  ccgaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTaccgc                                >  1:3481542/1‑68 (MQ=255)
                                  ccgaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTaccgc                                >  1:426570/1‑68 (MQ=255)
                                   cgaccgGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTAccacca                              <  1:766822/71‑1 (MQ=255)
                                   cgaccgGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTAccacca                              <  1:3918109/71‑1 (MQ=255)
                                   cgaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTAccgcca                              <  1:4751028/71‑1 (MQ=255)
                                    gaccgGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTacca                                 >  1:3642065/1‑67 (MQ=255)
                                    gaccgGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTAccacca                              >  1:1116641/1‑70 (MQ=255)
                                    gaccgGGCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTAccgcca                              <  1:3716781/70‑1 (MQ=255)
                                        gggCAGGATGCGCCGTGACGTGGCAGACGGATAAcgcg                                                          <  1:807345/38‑1 (MQ=25)
                                         ggCAGGATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTacc                                  >  1:5363327/1‑61 (MQ=255)
                                           cAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTAttt                                     <  1:868233/56‑1 (MQ=255)
                                           cAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTgcg                       >  1:1080147/1‑70 (MQ=255)
                                            aGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCaa                             <  1:5593544/63‑1 (MQ=255)
                                             ggATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGt                                                  <  1:127455/41‑1 (MQ=255)
                                             ggATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGt                                                  <  1:496128/41‑1 (MQ=255)
                                             ggATGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTgcgcgc                    <  1:4035730/71‑3 (MQ=255)
                                              gATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCAcc                   >  1:3962549/1‑71 (MQ=255)
                                              gATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCAcc                   <  1:4296266/71‑1 (MQ=255)
                                                tGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTa                                    >  1:1404639/1‑52 (MQ=255)
                                                tGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCAcc                   >  1:1704618/1‑69 (MQ=255)
                                                tGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTa                                    >  1:3483944/1‑52 (MQ=255)
                                                tGCGCCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGcc                   >  1:3596755/1‑69 (MQ=255)
                                                  cgcCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCaaa                            >  1:4584156/1‑58 (MQ=255)
                                                  cgcCGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAg                <  1:3368764/70‑1 (MQ=255)
                                                    ccGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTa                                        <  1:3373173/44‑1 (MQ=255)
                                                    ccGTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAcc             <  1:2376671/71‑1 (MQ=255)
                                                      gTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGAc              >  1:4623788/1‑68 (MQ=255)
                                                      gTGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGt                                         <  1:3361534/41‑1 (MQ=19)
                                                       tGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTg                         <  1:2570077/56‑1 (MQ=255)
                                                       tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGAc              <  1:502631/67‑1 (MQ=255)
                                                       tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAg          >  1:4065708/1‑71 (MQ=255)
                                                       tGACGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAg          >  1:2578522/1‑71 (MQ=255)
                                                         aCGTGGCAGGCGAATCACGCGGATGTCGTGAGCGaa                                           >  1:2317324/1‑36 (MQ=255)
                                                         aCGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAAc                           >  1:1413253/1‑52 (MQ=255)
                                                         aCGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAt        >  1:2604271/1‑71 (MQ=255)
                                                         aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgtt        <  1:5281815/71‑3 (MQ=255)
                                                         aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgtt        <  1:4418975/71‑3 (MQ=255)
                                                         aCGTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAgt         <  1:2940748/70‑2 (MQ=255)
                                                          cGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCaa                             <  1:4456709/49‑1 (MQ=255)
                                                          cGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCaa                             <  1:4795824/49‑1 (MQ=255)
                                                          cGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCaa                             <  1:2038483/49‑1 (MQ=255)
                                                           gTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAttt      <  1:1041444/71‑1 (MQ=255)
                                                           gTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAttt      <  1:2163767/71‑1 (MQ=255)
                                                           gTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTac                                   >  1:5358333/1‑42 (MQ=19)
                                                           gTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTa                                    >  1:5089089/1‑41 (MQ=19)
                                                           gTGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTAccgcca                              <  1:2535727/47‑1 (MQ=255)
                                                            tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTAtt                                      <  1:404026/38‑1 (MQ=255)
                                                            tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTAt                                       <  1:653327/37‑1 (MQ=255)
                                                            tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt     <  1:2860717/71‑1 (MQ=255)
                                                            tGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt     <  1:3543896/71‑1 (MQ=255)
                                                            tGGCAGACGGATAACGCGAATGTCGTGCGCGAAGTATTTACCGCCAAACTGCGCGCCAAGACCGAGtttct     <  1:2047092/71‑3 (MQ=255)
                                                                  gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtttt     <  1:5482134/65‑1 (MQ=255)
                                                                  gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtt       <  1:2112087/63‑1 (MQ=255)
                                                                  gCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGAtt       <  1:2447383/63‑1 (MQ=255)
                                                                  |                                                                   
GATATTACGGTCAGCAGAGCAGGAGACGCCCATACCGACCGGGCAGGATGCGCCGTGACGTGGCAGGCGAATCACGCGGATGTCGTGAGCGAAGTATTTACCACCAAACTGCGCACCCAGACCAAGATTTTGCG  >  minE/1015097‑1015230

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