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 F21 I0 R2 370 72.1 3738297 91.5% 3420541 62.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,015,013 T→C 5.7% K352K (AAA→AAG) ‡ fumA ← aerobic Class I fumarate hydratase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,015,0130TC 5.7% 204.0 / 3.3 70K352K (AAA→AAG) ‡fumAaerobic Class I fumarate hydratase
Reads supporting (aligned to +/- strand):  ref base T (40/26);  new base C (2/2);  total (42/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

CGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGG  >  minE/1014944‑1015082
                                                                     |                                                                     
cGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCtt                                                                      >  1:2769861/1‑71 (MQ=255)
cGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCtt                                                                      >  1:1511815/1‑71 (MQ=255)
     aCTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgcgc                                                                 <  1:2601979/71‑1 (MQ=255)
     aCTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgcgc                                                                 <  1:1130963/71‑1 (MQ=255)
     aCTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgcgc                                                                 <  1:2328628/71‑1 (MQ=255)
      cTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTgcg                                                                  >  1:2016792/1‑69 (MQ=255)
      cTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCa                                                                <  1:3349773/71‑1 (MQ=255)
         tgCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCt                                                                       >  1:3527561/1‑61 (MQ=255)
         tgCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCt                                                                       >  1:104038/1‑61 (MQ=255)
         ggCGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAg                                                               <  1:1030279/68‑1 (MQ=255)
         ggCGAGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAg                                                               <  1:1343560/68‑1 (MQ=255)
          gCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAg                                                               >  1:631981/1‑68 (MQ=255)
          gCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAg                                                               >  1:748520/1‑68 (MQ=255)
            gAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCtt                                                          <  1:3063775/71‑1 (MQ=255)
             aGGATCTCTTTCATCGGGCGGTTAAGGTCAACTTTCACCGCTTCGCCTTCACCGGCCTGGCGCAGTTCtt                                                          >  1:1855914/1‑70 (MQ=255)
                    ctTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGata                                                  >  1:2459057/1‑71 (MQ=255)
                        cATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATAtt                                              >  1:63896/1‑71 (MQ=255)
                          tCGGCCGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCttt                                                                     >  1:3594273/1‑46 (MQ=255)
                             gACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                             >  1:2682248/1‑51 (MQ=255)
                             gACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                             >  1:153172/1‑51 (MQ=255)
                             gACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                             >  1:2064079/1‑51 (MQ=255)
                             gACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                             >  1:2854320/1‑51 (MQ=255)
                             gACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                             >  1:2115966/1‑51 (MQ=255)
                             gACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGct                                                             >  1:3575326/1‑51 (MQ=255)
                                ggTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGctct                                                           >  1:791765/1‑50 (MQ=255)
                                ggTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGa                                      >  1:2552956/1‑71 (MQ=255)
                                ggTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGa                                      <  1:101887/71‑1 (MQ=255)
                                ggTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGa                                      >  1:1037324/1‑71 (MQ=255)
                                ggTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGa                                      <  1:3021412/71‑1 (MQ=255)
                                 gTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGAt                                     >  1:277053/1‑71 (MQ=255)
                                  ttAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCt                                         >  1:72550/1‑66 (MQ=255)
                                    aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTa                                   >  1:864469/1‑70 (MQ=255)
                                    aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTAt                                  >  1:2468755/1‑71 (MQ=255)
                                    aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTAt                                  >  1:3604986/1‑71 (MQ=255)
                                    aaGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTAt                                  >  1:3326918/1‑71 (MQ=255)
                                       gTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGc                                           >  1:3235785/1‑59 (MQ=255)
                                         cAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTc                              >  1:2472784/1‑70 (MQ=255)
                                          aaCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTc                              >  1:1533975/1‑69 (MQ=255)
                                           aCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGa                                                    >  1:107726/1‑46 (MQ=255)
                                           aCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTgg                                       <  1:1871485/59‑1 (MQ=255)
                                           aCGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAg                           >  1:1115247/1‑71 (MQ=255)
                                               gcACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCt                                         <  1:3377057/53‑1 (MQ=255)
                                               gcACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtttt                       <  1:1173949/71‑1 (MQ=255)
                                               gcACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGttt                        <  1:2481363/70‑1 (MQ=255)
                                                cACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGa                                      >  1:822647/1‑55 (MQ=255)
                                                 aCCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTT‑CGGGATATATTTGCCTGGAt                                     >  1:313294/1‑54 (MQ=255)
                                                   cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTa                                   <  1:3409092/55‑1 (MQ=255)
                                                   cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                   >  1:1790885/1‑71 (MQ=255)
                                                   cGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGa                   >  1:1733483/1‑71 (MQ=255)
                                                   cGCTTCGCCTTCACCGGCCTGGCGCAGTTCTTGTGGAATGTACTGGCCTGGGTTGTGTTCCAGTTTTTCGa                   >  1:300801/1‑71 (MQ=255)
                                                     cTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                 <  1:1488023/71‑1 (MQ=255)
                                                     cTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                 <  1:1584317/71‑1 (MQ=255)
                                                     cTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                 <  1:1503420/71‑1 (MQ=255)
                                                      ttCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                 >  1:2505800/1‑70 (MQ=255)
                                                      ttCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                 >  1:3388839/1‑70 (MQ=255)
                                                        cGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATcc                <  1:3089084/69‑1 (MQ=255)
                                                        cGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATcc                <  1:3696851/69‑1 (MQ=255)
                                                         gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAg              <  1:1665220/70‑1 (MQ=255)
                                                         gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGa             <  1:2498920/71‑1 (MQ=255)
                                                         gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGa             <  1:3076572/71‑1 (MQ=255)
                                                         gCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGa             <  1:1218377/71‑1 (MQ=255)
                                                          ccTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtttt                       <  1:3114930/60‑1 (MQ=255)
                                                           cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCt                                         <  1:2966203/41‑1 (MQ=255)
                                                           cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCt                                         <  1:3688761/41‑1 (MQ=255)
                                                           cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc           >  1:2106102/1‑71 (MQ=255)
                                                           cTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATc           >  1:3171282/1‑71 (MQ=255)
                                                            ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCt                                         <  1:2998469/40‑1 (MQ=255)
                                                            ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGtttt                       >  1:1233957/1‑58 (MQ=255)
                                                            ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATc                 >  1:1292118/1‑64 (MQ=255)
                                                            ttCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGAt            >  1:972872/1‑69 (MQ=255)
                                                              ctcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGa                                      >  1:3016646/1‑41 (MQ=255)
                                                               tcCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCt       >  1:691334/1‑71 (MQ=255)
                                                                cccGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCt       >  1:3036100/1‑70 (MQ=255)
                                                                  cGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGAc    >  1:2917931/1‑71 (MQ=255)
                                                                    cTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACgg  <  1:3614383/71‑1 (MQ=255)
                                                                     |                                                                     
CGACAACTGTGCGAGGATCTCTTTCATCGGACGGTTAAGGTCAACGCGCACCGCTTCGCCTTCTCCCGCTTTGCGCAGCTCTTCCGGGATATATTTGCCTGGATTATGTTCCAGTTTTTCGATCCAGATCCCCTGACGG  >  minE/1014944‑1015082

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