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 1,014,677 G→A 25.4% G464G (GGC→GGT)  fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,014,6770GA25.4% 97.9 / 31.6 59G464G (GGC→GGT) fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base G (19/25);  new base A (7/8);  total (26/33)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCG  >  minE/1014609‑1014746
                                                                    |                                                                     
ccgccGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTAcc                                                                     >  1:1428085/4‑71 (MQ=255)
   ccGATGCTACCGAGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCttt                                                                  <  1:2124863/71‑1 (MQ=255)
      aTACTGCCGAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGc                                                               >  1:4718648/1‑71 (MQ=255)
            ccgaGGTAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCAt                                                         >  1:4711726/4‑71 (MQ=255)
             cAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATg                                                        <  1:3314451/71‑1 (MQ=255)
              aaGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGa                                                       <  1:4642660/71‑1 (MQ=255)
                 gTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGc                                                               >  1:9102/1‑60 (MQ=255)
                 gTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCa                                                    <  1:2046162/71‑1 (MQ=255)
                  tAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCa                                                    >  1:2626776/1‑70 (MQ=255)
                  tAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                                                   <  1:887462/71‑1 (MQ=255)
                  tAGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAt                                                   <  1:2955299/71‑1 (MQ=255)
                   aGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                                                   >  1:2383907/1‑70 (MQ=255)
                   aGAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtg                                                  >  1:875607/1‑70 (MQ=255)
                    gAAGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtg                                                  <  1:2329419/70‑2 (MQ=255)
                     aaGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtgc                                                 <  1:3357362/70‑3 (MQ=255)
                     aaGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCAtg                                                  <  1:3328683/69‑2 (MQ=255)
                     aaGCCGCCGTGTTTATGACACGCGTCGGTAACCTGCTGACTGCGGTTACCTTTCGCCAGCATGATCATGCt                                                <  1:530231/71‑1 (MQ=255)
                         cgccgTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg                                            >  1:4858543/1‑71 (MQ=255)
                         cgccgTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg                                            <  1:5149872/71‑1 (MQ=255)
                         cgccgTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg                                            <  1:4932291/71‑1 (MQ=255)
                              tgtTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                                                   <  1:4861554/59‑1 (MQ=255)
                              tgtTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                                                   <  1:4868250/59‑1 (MQ=255)
                                ttttttACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCAt                                                   <  1:4304837/57‑1 (MQ=255)
                                 tttttACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTgcgc                                    >  1:3348219/1‑71 (MQ=255)
                                  ttttACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTc                                                                 <  1:328727/41‑1 (MQ=255)
                                     tACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTg                                 <  1:2412482/70‑1 (MQ=255)
                                     tACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTg                                 >  1:118167/1‑70 (MQ=255)
                                       cAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGc                                <  1:3500963/69‑1 (MQ=255)
                                       cAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCa                               <  1:1257073/70‑1 (MQ=255)
                                           cATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGa                          >  1:1866316/1‑71 (MQ=255)
                                            aTCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGAt                         >  1:785037/1‑71 (MQ=255)
                                               cGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATAc                                                 >  1:3708461/1‑44 (MQ=255)
                                               cGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATAc                                                 >  1:3604764/1‑44 (MQ=255)
                                                gTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg                                            <  1:5680458/48‑1 (MQ=255)
                                                gTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCg                                            <  1:5604358/48‑1 (MQ=255)
                                                gTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCa                               >  1:72032/1‑61 (MQ=255)
                                                   aCCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACAt                   >  1:2767763/1‑70 (MQ=255)
                                                       gctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGaa              >  1:3249287/1‑71 (MQ=255)
                                                       gctgactgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGag              >  1:472056/1‑70 (MQ=255)
                                                        ctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTg                           <  1:349343/57‑1 (MQ=255)
                                                        ctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGa               <  1:3328560/69‑1 (MQ=255)
                                                        ctggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCAACATAAGa               <  1:2458362/69‑1 (MQ=255)
                                                        ctgactgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTa                  >  1:5578970/1‑66 (MQ=255)
                                                          ggctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGc                                >  1:538187/1‑50 (MQ=255)
                                                          gactgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtc            >  1:2740101/3‑70 (MQ=255)
                                                            ctgCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatccat         >  1:919753/1‑71 (MQ=255)
                                                            ctgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtccat         <  1:635382/71‑1 (MQ=255)
                                                             tgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCAcgt                   <  1:5649444/60‑3 (MQ=255)
                                                             tgCGGTTACCTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtccata        >  1:33357/1‑70 (MQ=255)
                                                              gCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatccatcc       >  1:4892227/1‑71 (MQ=255)
                                                                 gTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatcca          <  1:3370554/65‑1 (MQ=255)
                                                                  ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAg                              <  1:5237625/44‑1 (MQ=255)
                                                                  ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAg                              <  1:4838559/44‑1 (MQ=255)
                                                                  ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAg                              <  1:4813594/44‑1 (MQ=255)
                                                                  ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAg                              <  1:469002/44‑1 (MQ=255)
                                                                  ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAg                              <  1:1075610/44‑1 (MQ=255)
                                                                  ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgtcc   >  1:2943055/1‑71 (MQ=255)
                                                                  ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCATGCAg                              <  1:4093900/44‑1 (MQ=255)
                                                                   tGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgtccg  >  1:2437893/1‑71 (MQ=255)
                                                                    gCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgtccg  >  1:153873/1‑70 (MQ=255)
                                                                    gCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgt     <  1:4345819/67‑1 (MQ=255)
                                                                    |                                                                     
CCACCGATACTGCCAAGGTAGAAGCCGCCGTGTTTTTTACAGGCATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCG  >  minE/1014609‑1014746

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