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 1,758,115 T→G 28.0% G106G (GGA→GGC)  kgtP ← alpha‑ketoglutarate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,758,1150TG28.0% 179.9 / 95.7 150G106G (GGA→GGC) kgtPalpha‑ketoglutarate transporter
Reads supporting (aligned to +/- strand):  ref base T (76/32);  new base G (18/24);  total (94/56)
Fisher's exact test for biased strand distribution p-value = 2.52e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 150 total aligned reads displayed.

AATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAT  >  minE/1758056‑1758177
                                                           |                                                              
aatGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:2383072/1‑69 (MQ=255)
aatGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:163157/1‑69 (MQ=255)
aatGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:3106573/1‑69 (MQ=255)
aatGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:3233876/1‑69 (MQ=255)
aatGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAac                                                         >  1:908835/1‑67 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGa                                                            >  1:1618831/1‑63 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:1033122/1‑68 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:1840072/1‑68 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:2394554/1‑68 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:2395450/1‑68 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:2984031/1‑68 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAaca                                                        >  1:2090657/1‑67 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGAAGGCGATAACCAGGGATCCGAAacac                                                       >  1:1962223/1‑68 (MQ=255)
    ccGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGTGATAACCAGCGATCCGAAACAcatca                                                   <  1:808794/69‑1 (MQ=255)
    ccGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatca                                                   <  1:1390658/69‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatcat                                                  <  1:3052845/68‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATa                                                 <  1:3423622/69‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATa                                                 <  1:3409796/69‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATa                                                 <  1:49933/69‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATa                                                 <  1:605003/69‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATa                                                 <  1:1151722/69‑1 (MQ=255)
       gAGGCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2810531/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2480926/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:205484/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2254229/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:98346/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2339003/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1000132/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:714307/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:3042130/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:465003/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:361066/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:354405/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1545851/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1543418/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1340398/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:172238/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1801961/1‑68 (MQ=255)
       gAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatcat                                                  <  1:2059023/67‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:2922221/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:296161/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:2533292/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:2451412/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:1503160/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:1471157/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:2070324/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:1955310/54‑1 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATac                                                >  1:1812239/1‑59 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:3344640/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:381261/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1516202/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1214427/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1143021/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:3006391/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1060043/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1610561/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:2589359/1‑67 (MQ=255)
                  ccTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcat                                                     >  1:3000637/1‑53 (MQ=255)
                  ccTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAAc                                     >  1:848054/1‑69 (MQ=255)
                       aGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCa                                 >  1:9438/1‑68 (MQ=255)
                       aGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCa                                 >  1:3257516/1‑68 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2888167/1‑69 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2831569/1‑69 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2970663/1‑69 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2240262/1‑69 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2325413/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:1502366/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:1516996/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:1135543/1‑59 (MQ=255)
                                         gcaggcGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATg              >  1:2487784/1‑69 (MQ=255)
                                         gcaggcGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATg              >  1:555529/1‑69 (MQ=255)
                                         gcaggcGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATg              >  1:1627797/1‑69 (MQ=255)
                                         gcaggcGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATg              >  1:2883244/1‑69 (MQ=255)
                                             gcGATAACCAGTGAGCCGAAACGCATCATACACACCGATa                                       <  1:773832/40‑1 (MQ=25)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:3419414/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:861234/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:433618/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:98185/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:36931/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:1390191/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:1697799/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:3029291/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:3183467/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:2445207/40‑1 (MQ=37)
                                              cGATAAACAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:1123503/39‑1 (MQ=37)
                                                aTAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCg       <  1:1846454/69‑1 (MQ=255)
                                                  aaCCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCTACCATGTTTATCGGc     >  1:576959/1‑69 (MQ=255)
                                                  aaCCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGc     >  1:3284193/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:195369/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:1979196/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:2931814/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:2774746/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:2995611/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:749027/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:1484355/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:3330150/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:1340602/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:401237/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:2304681/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:284292/1‑69 (MQ=255)
                                                           |                                                              
AATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAT  >  minE/1758056‑1758177

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