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 1,758,112 C→T 28.5% S107S (TCG→TCA)  kgtP ← alpha‑ketoglutarate transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,758,1120CT28.5% 165.3 / 65.3 151S107S (TCG→TCA) kgtPalpha‑ketoglutarate transporter
Reads supporting (aligned to +/- strand):  ref base C (75/32);  new base T (19/24);  total (95/56)
Fisher's exact test for biased strand distribution p-value = 4.79e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 151 total aligned reads displayed.

AATGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAT  >  minE/1758056‑1758177
                                                        |                                                                 
aatGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:809246/1‑69 (MQ=255)
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)
 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)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAaca                                                        >  1:2090657/1‑67 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGAAGGCGATAACCAGGGATCCGAAacac                                                       >  1:1962223/1‑68 (MQ=255)
 atGCCGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGCCAGGCGATAACCAGCGATCCGAAacac                                                       >  1:2865128/1‑68 (MQ=255)
    ccGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGTGATAACCAGCGATCCGAAACAcatca                                                   <  1:808794/69‑1 (MQ=255)
    ccGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatca                                                   <  1:3251512/69‑1 (MQ=255)
    ccGGAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatca                                                   <  1:1390658/69‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatcat                                                  <  1:3026136/68‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatcat                                                  <  1:2595710/68‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATa                                                 <  1:605003/69‑1 (MQ=255)
      ggAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATa                                                 <  1:1151722/69‑1 (MQ=255)
       gAGGCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2810531/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:98346/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:205484/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1000132/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:888680/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2254229/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2339003/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:465003/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:354405/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:2480926/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:3042130/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1545851/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1543418/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1801961/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:172238/1‑68 (MQ=255)
       gAGCCCAGGTACCGATTGTTTCGTAGCCTGGCAAACAGGCGATAACCAGTGAGCCGAAACACATCATa                                                 >  1:1340398/1‑68 (MQ=255)
       gAGCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACAcatcat                                                  <  1:2059023/67‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:576356/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:2451412/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:2533292/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:3422946/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:1471157/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:1503160/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:2070324/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:1955310/54‑1 (MQ=255)
         gCCCACGTACCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCg                                                             <  1:944022/54‑1 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATac                                                >  1:1812239/1‑59 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:381261/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1516202/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:330398/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:3344640/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:36059/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:3006391/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1214427/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1143021/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1060043/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:1610561/1‑67 (MQ=255)
                 aCCTATAGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGAt                                        >  1:2589359/1‑67 (MQ=255)
                       aGTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCa                                 >  1:9438/1‑68 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2888167/1‑69 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:689224/1‑69 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2240262/1‑69 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2896572/1‑69 (MQ=255)
                        gTTTCATAACCTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2970663/1‑69 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:1135543/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:1516996/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:1502366/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:3048605/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:416543/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:476512/1‑59 (MQ=255)
                                  cTGGGAGGCAGGCGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATc                               >  1:2325413/1‑59 (MQ=255)
                                         gcaggcGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATg              >  1:555529/1‑69 (MQ=255)
                                         gcaggcGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATg              >  1:1627797/1‑69 (MQ=255)
                                         gcaggcGATAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATg              >  1:2487784/1‑69 (MQ=255)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:3419414/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:861234/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:1697799/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:36931/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:766753/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:2953419/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:3378915/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:2445207/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:1390191/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:3123613/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:2811413/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:2999538/40‑1 (MQ=37)
                                             gcGATAACCAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:2972212/40‑1 (MQ=37)
                                              cGATAAACAGTGAGCCGAAACACATCATACACACCGATa                                       <  1:1123503/39‑1 (MQ=37)
                                                aTAACCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCg       <  1:1846454/69‑1 (MQ=255)
                                                  aaCCAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGc     >  1:3284193/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:284292/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:195369/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:1979196/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:749027/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:2931814/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:2304681/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:401237/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:1340602/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:1484355/1‑69 (MQ=255)
                                                     cAGCGATCCGAAACACATCATACACACCGATAACAGCATCGATTTTTTGCGACCATGTTTATCGGCTAt  >  1:2995611/1‑69 (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