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 1,014,719 T→C 23.2% Q450Q (CAA→CAG) ‡ fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,014,7190TC23.2% 149.4 / 45.3 86Q450Q (CAA→CAG) ‡fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base T (39/27);  new base C (11/9);  total (50/36)
Fisher's exact test for biased strand distribution p-value = 7.99e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01

CATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCC  >  minE/1014652‑1014785
                                                                   |                                                                  
cATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGa                                                                 >  1:1866316/1‑71 (MQ=255)
 aTCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGAt                                                                >  1:785037/1‑71 (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)
               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)
                       ttGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgtcc                                          >  1:2943055/1‑71 (MQ=255)
                        taccTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCAtacggcct                                         >  1:2604965/3‑70 (MQ=255)
                        tGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgtccg                                         >  1:2437893/1‑71 (MQ=255)
                         gCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgtccg                                         >  1:153873/1‑70 (MQ=255)
                         gCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccgt                                            <  1:4345819/67‑1 (MQ=255)
                         accTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCAtacggcctg                                        >  1:3405713/2‑69 (MQ=255)
                         accTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCAtacggcctg                                        >  1:5384115/2‑69 (MQ=255)
                         accTTTCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCAtacggcctg                                        >  1:3270859/2‑69 (MQ=255)
                         accTTTCGCCAGCATGATCATGCCGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCAtacggcct                                         >  1:5142767/2‑69 (MQ=255)
                           cTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCcggcg                                      >  1:2273606/1‑71 (MQ=255)
                            tttCGCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAgtcca                                                 <  1:4624087/59‑1 (MQ=255)
                             ttCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGt                                    >  1:3373890/1‑71 (MQ=255)
                              tCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACa                                                           >  1:2347324/1‑47 (MQ=255)
                              tCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACa                                                           >  1:1007613/1‑47 (MQ=255)
                              tCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGt                                    <  1:1482870/70‑1 (MQ=255)
                              tCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTc                                   >  1:4617686/1‑71 (MQ=255)
                                gCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCggtggt                                 <  1:208187/71‑1 (MQ=255)
                                gCCAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGtg                                   <  1:2335407/69‑2 (MQ=255)
                                gCCAGCATGATCATACTTCCGCCCTGCGCTAGCAGTTGATCGACATAAGaa                                                     >  1:179943/1‑51 (MQ=255)
                                 ccAGCATGATCATGCTGCCGCCGTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGtt                                <  1:5185377/71‑1 (MQ=255)
                                 ccAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatc                                                   <  1:3114174/52‑1 (MQ=255)
                                 ccAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCAtccg                                             <  1:5585939/58‑1 (MQ=255)
                                 ccAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGt                                 <  1:3198675/70‑1 (MQ=255)
                                   aGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTgg                              >  1:1936462/1‑71 (MQ=255)
                                   aGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTgg                              <  1:3163240/71‑1 (MQ=255)
                                     cATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGt                                 <  1:5507567/66‑1 (MQ=255)
                                     cATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGc                            >  1:2295277/1‑71 (MQ=255)
                                       tgttCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCa                          <  1:3217070/68‑1 (MQ=255)
                                       tGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATa                                                         <  1:4895398/40‑1 (MQ=255)
                                       tGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATa                                                         <  1:469015/40‑1 (MQ=255)
                                       tGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATa                                                         <  1:2032453/40‑1 (MQ=255)
                                       tGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTg                               >  1:1444583/1‑66 (MQ=255)
                                       tGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGcc                           <  1:4603298/70‑1 (MQ=255)
                                        gATCATACTTCCGCCCTGTGCTTGCAGTTGATCGACATAAGaa                                                     <  1:1828306/43‑1 (MQ=255)
                                        gATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGtt                                <  1:2871881/64‑1 (MQ=255)
                                         aTCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatccatcc                                              >  1:2968097/1‑49 (MQ=255)
                                         aTCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAatccatcc                                              >  1:3933305/1‑49 (MQ=255)
                                         aTCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAat                                                    <  1:3905659/43‑1 (MQ=255)
                                         aTCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAat                                                    <  1:4334084/43‑1 (MQ=255)
                                         aTCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAat                                                    <  1:430467/43‑1 (MQ=255)
                                         aTCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGcc                           >  1:520481/1‑68 (MQ=255)
                                          tCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAg                                                       <  1:5372804/39‑1 (MQ=255)
                                          tCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAg                                                       <  1:1640576/39‑1 (MQ=255)
                                          tCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAg                                                       <  1:1201293/39‑1 (MQ=255)
                                          tCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCg                                  >  1:4616898/1‑60 (MQ=255)
                                            aTACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAagag                      >  1:5288592/1‑70 (MQ=255)
                                              aCTTCCGCCCTGCGCTTGCAGTTGATCGACATAAg                                                       >  1:276670/1‑35 (MQ=255)
                                              aCTTCCGCCCTGCGCTTGCAGTTGATCGACATAAg                                                       >  1:917123/1‑35 (MQ=255)
                                               ctgccgccgTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAAc                   >  1:1768185/4‑70 (MQ=255)
                                                 tCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCg                 >  1:3303521/1‑70 (MQ=255)
                                                  ccgccgTGGGATTGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAAcctg                <  1:2496049/70‑3 (MQ=255)
                                                  ccGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCAGTCCGGCGGTCGTTGGGCCAAGAGAACCg                 >  1:532879/1‑69 (MQ=255)
                                                   cGCCCTGCGCTTGCAGTTGATCGACATAAGAatcca                                                 >  1:1688855/1‑36 (MQ=255)
                                                   cGCCCTGCGCTTGCAGTTGATCGACATAAGAatcca                                                 >  1:4922593/1‑36 (MQ=255)
                                                       cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga                       >  1:3284340/1‑58 (MQ=255)
                                                       cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga                       >  1:73698/1‑58 (MQ=255)
                                                       cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga                       >  1:5226654/1‑58 (MQ=255)
                                                       cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga                       >  1:3919429/1‑58 (MQ=255)
                                                       cTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAaga                       >  1:2758279/1‑58 (MQ=255)
                                                             ttGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGt                                 <  1:1779207/42‑1 (MQ=255)
                                                             ttGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAAcctg                <  1:2145841/59‑3 (MQ=255)
                                                              tGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTc   >  1:1543561/1‑71 (MQ=255)
                                                              tGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAgtga                     <  1:5144256/53‑1 (MQ=255)
                                                              tGCAGCAGATCCACGTAGGAGTCCATACGGCCTGCGGTGGTTGGGCCAAGTGAACCTGATGGATAAccgg    >  1:3406880/1‑68 (MQ=255)
                                                               gCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCg                                  <  1:3510167/39‑1 (MQ=255)
                                                               gCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCg                                  <  1:2092348/39‑1 (MQ=255)
                                                               gCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGt                                 >  1:61690/1‑40 (MQ=255)
                                                               gCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGt                                 >  1:1125083/1‑40 (MQ=255)
                                                               gCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGt                                 >  1:1098524/1‑40 (MQ=255)
                                                               gCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTcc  >  1:2276558/1‑71 (MQ=255)
                                                                   ttGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCaa                         <  1:3044223/44‑1 (MQ=255)
                                                                   ttGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCaa                         <  1:2636206/44‑1 (MQ=255)
                                                                   |                                                                  
CATCCGTCACCTGCTGGCTGCGGTTGCCTTTCGCCAGCATGATCATACTTCCGCCCTGCGCTTGCAGTTGATCGACATAAGAATCCATCCGTCCGGCGGTCGTTGGGCCAAGAGAACCGGAGGCATAACCTTCC  >  minE/1014652‑1014785

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