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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 2,439,903 T→C 25.4% P247P (CCA→CCG)  ilvC ← ketol‑acid reductoisomerase, NAD(P)‑binding

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE2,439,9030TC25.4% 109.8 / 34.6 94P247P (CCA→CCG) ilvCketol‑acid reductoisomerase, NAD(P)‑binding
Reads supporting (aligned to +/- strand):  ref base T (37/33);  new base C (8/16);  total (45/49)
Fisher's exact test for biased strand distribution p-value = 1.55e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CCGCCCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGAGCCAGCC  >  minE/2439838‑2439954
                                                                 |                                                   
ccgccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTgg                                                   >  1:2072169/1‑68 (MQ=255)
ccgccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGa                                                  >  1:2049960/1‑69 (MQ=255)
ccgccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGa                                                  >  1:2815516/1‑69 (MQ=255)
ccgccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGa                                                  >  1:1724285/1‑69 (MQ=255)
  gccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGAt                                                 <  1:1079438/68‑1 (MQ=255)
  gccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGAt                                                 <  1:2092296/68‑1 (MQ=255)
  gccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGAt                                                 <  1:2915247/68‑1 (MQ=255)
  gccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGAt                                                 <  1:460108/68‑1 (MQ=255)
  gccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGAt                                                 <  1:1473406/68‑1 (MQ=255)
  gccCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATACTGGAt                                                 <  1:1898410/68‑1 (MQ=255)
   tccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:1351617/2‑69 (MQ=255)
   cccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:731974/1‑69 (MQ=255)
   cccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:2287509/1‑69 (MQ=255)
   cccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:1586482/1‑69 (MQ=255)
   cccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:2530866/1‑69 (MQ=255)
   cccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:1278535/1‑69 (MQ=255)
   cccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:2822624/1‑69 (MQ=255)
   cccTGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCg                                               >  1:1298570/1‑69 (MQ=255)
     cTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGt                                             <  1:3154662/69‑1 (MQ=255)
     cTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGt                                             <  1:2409342/69‑1 (MQ=255)
     cTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGt                                             <  1:2514619/69‑1 (MQ=255)
     cTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGt                                             <  1:138436/69‑1 (MQ=255)
     cTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGt                                             <  1:1308839/69‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:3160728/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:3268554/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:760880/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:3428429/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:3430442/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:2635587/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:355928/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:454534/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:506530/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:655999/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:839670/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:878800/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:1091625/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:1687580/68‑1 (MQ=255)
      tGTTTCAGCGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:1232043/68‑1 (MQ=255)
       gTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTAc                                           >  1:638253/1‑69 (MQ=255)
          tCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACct                                         <  1:2600827/68‑1 (MQ=255)
            aGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACcttc                                       <  1:2308419/68‑1 (MQ=255)
              tGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGt                                             <  1:2869690/60‑1 (MQ=255)
                           gTTTCCGAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:437465/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCttcttc                                    >  1:905948/1‑56 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:485682/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:474596/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:450431/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:222996/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:388188/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:829121/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:1625490/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:1677736/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:3394692/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:1111810/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:1688104/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:2918617/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:2913515/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:2101682/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:1749805/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:2767714/1‑67 (MQ=255)
                           gTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGt                         >  1:2762441/1‑67 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGa                                                  >  1:2506806/1‑40 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACcttc                                       >  1:160617/1‑51 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:251794/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:2333583/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:12831/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:1422321/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:1528567/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:1581703/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:1833946/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:1819214/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:2851895/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:2797660/1‑68 (MQ=255)
                             ttCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGa                      >  1:2787992/1‑68 (MQ=255)
                              tCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAg                    <  1:1915971/69‑1 (MQ=255)
                              tCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAg                    <  1:185527/69‑1 (MQ=255)
                              tCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAg                    <  1:1591746/69‑1 (MQ=255)
                              tCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAg                    <  1:2971222/69‑1 (MQ=255)
                              tCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAg                    <  1:671137/69‑1 (MQ=255)
                                 cAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCttcttc                                    <  1:3061453/50‑1 (MQ=255)
                                 cAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCttcttc                                    <  1:682178/50‑1 (MQ=255)
                                 cAACCGAACTGAATCAGTTTTTCTGCGTATGCCGGATCGGt                                             <  1:2001144/41‑1 (MQ=255)
                                     cGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCAcagca             <  1:271318/69‑1 (MQ=255)
                                     cGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCAcagca             <  1:2495567/69‑1 (MQ=255)
                                     cGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCAcagca             <  1:1683379/69‑1 (MQ=255)
                                         cTGAATCAGTTTTTCTGCGTATGCTGGATCGGTAGct                                         <  1:737276/37‑1 (MQ=255)
                                              tCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGagccag    <  1:473144/69‑1 (MQ=255)
                                              tCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGagccag    <  1:3130219/69‑1 (MQ=255)
                                              tCAGTTTTTCT‑‑GTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGagccag    <  1:3226652/67‑1 (MQ=255)
                                               cAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGagccag    <  1:1530731/68‑1 (MQ=255)
                                               cAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGagccag    <  1:1797022/68‑1 (MQ=255)
                                                aGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGagccagcc  <  1:2497173/69‑1 (MQ=255)
                                                aGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGagccagcc  <  1:2693083/69‑1 (MQ=255)
                                                     ttCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAg                    <  1:1696221/46‑1 (MQ=255)
                                                                 |                                                   
CCGCCCTGTTTCAGTGCTTCGGTGATGGTTTCCCAACCGAACTGAATCAGTTTTTCTGCGTATGCTGGATCGGTACCTTCTTCCACCAGCTTGTCGAAGCACAGCAGAGAGCCAGCC  >  minE/2439838‑2439954

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