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 F8 I0 R2 296 77.6 4260404 88.1% 3753415 61.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 498,441 C→T 63.6% G24S (GGT→AGT)  galE ← UDP‑galactose‑4‑epimerase

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE498,4410CT63.6% 143.9 / 171.1 155G24S (GGT→AGT) galEUDP‑galactose‑4‑epimerase
Reads supporting (aligned to +/- strand):  ref base C (45/11);  new base T (51/47);  total (97/58)
Fisher's exact test for biased strand distribution p-value = 5.16e-04
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 156 total aligned reads displayed.

GCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCAT  >  minE/498375‑498510
                                                                  |                                                                     
gCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGttt                                                                   <  1:2129348/71‑1 (MQ=255)
gCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGttt                                                                   <  1:1288222/71‑1 (MQ=255)
gCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGttt                                                                   <  1:2927345/71‑1 (MQ=255)
 cTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtttt                                                                  <  1:1467982/71‑1 (MQ=255)
    gATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTg                                                                 <  1:2215895/69‑1 (MQ=255)
    gATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTg                                                                 >  1:2470091/1‑69 (MQ=255)
      tAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAg                                                              >  1:774819/1‑70 (MQ=255)
      tAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                             <  1:243357/71‑1 (MQ=255)
       aaCAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCa                                                               >  1:762001/1‑68 (MQ=255)
       aaCAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCa                                                               >  1:2023554/1‑68 (MQ=255)
        aCAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTaa                                                           >  1:3658529/1‑71 (MQ=255)
        aCAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTa                                                            <  1:2322295/70‑1 (MQ=255)
        aCAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTaa                                                           <  1:1941562/71‑1 (MQ=255)
        aCAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTaa                                                           <  1:3048310/71‑1 (MQ=255)
           ggCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGt                                                             <  1:2404745/66‑1 (MQ=255)
            gCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGt                                                                     <  1:2639009/57‑1 (MQ=255)
                tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtttt                                                                  >  1:2433885/1‑56 (MQ=255)
                tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtttt                                                                  >  1:254794/1‑56 (MQ=255)
                tACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGtttt                                                                  >  1:399288/1‑56 (MQ=255)
                 aCGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGcaca                                                    >  1:383384/1‑69 (MQ=255)
                  cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAg                                                 >  1:3156950/1‑71 (MQ=255)
                  cGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAg                                                 >  1:756181/1‑71 (MQ=255)
                   gCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                                <  1:17016/71‑1 (MQ=255)
                   gCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                                <  1:1644046/71‑1 (MQ=255)
                   gCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                                <  1:3455411/71‑1 (MQ=255)
                   gCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                                <  1:2473436/71‑1 (MQ=255)
                   gCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAgg                                                <  1:207714/71‑1 (MQ=255)
                   gCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAg                                                 >  1:3864423/1‑70 (MQ=255)
                     tGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGt                                                                     >  1:908670/1‑48 (MQ=255)
                     tGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCa                                                               >  1:1250373/1‑54 (MQ=255)
                     tGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCa                                                               >  1:2565144/1‑54 (MQ=255)
                       cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTaa                                                           >  1:3957433/1‑56 (MQ=255)
                       cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTaa                                                           >  1:405696/1‑56 (MQ=255)
                       cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTaa                                                           >  1:159604/1‑56 (MQ=255)
                       cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTAt                                             <  1:2159961/70‑1 (MQ=255)
                       cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTAt                                             <  1:4069814/70‑1 (MQ=255)
                       cgcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTAt                                             >  1:553987/1‑70 (MQ=255)
                        gcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTa                                                            <  1:3204987/54‑1 (MQ=255)
                        gcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTa                                                            <  1:490628/54‑1 (MQ=255)
                        gcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTa                                                            <  1:726558/54‑1 (MQ=255)
                        gcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                           <  1:1913355/71‑1 (MQ=255)
                        gcTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                           <  1:1198401/71‑1 (MQ=255)
                         cTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                           <  1:1719652/70‑1 (MQ=255)
                             cTGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTAt                                             <  1:609678/64‑1 (MQ=255)
                              tGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACt                                         <  1:3172752/67‑1 (MQ=255)
                              tGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACt                                         <  1:1424833/67‑1 (MQ=255)
                              tGTTACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACt                                         <  1:2066520/67‑1 (MQ=255)
                              tGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGcaca                                                    >  1:2599546/1‑56 (MQ=255)
                              tGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGcaca                                                    >  1:532055/1‑56 (MQ=255)
                                ttACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTc                                       >  1:2057265/1‑67 (MQ=255)
                                ttACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTc                                       >  1:752860/1‑67 (MQ=255)
                                ttACAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTc                                       >  1:1162908/1‑67 (MQ=255)
                                ttACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGt                                                             <  1:3122987/45‑1 (MQ=255)
                                  aCAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATg                                  >  1:2936161/1‑70 (MQ=255)
                                  aCAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTc                                       >  1:2214547/1‑65 (MQ=255)
                                   cAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                           >  1:1480535/1‑60 (MQ=255)
                                   cAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGa                                           >  1:559277/1‑60 (MQ=255)
                                   cAGAGGTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTa                                <  1:2827348/71‑1 (MQ=255)
                                   cAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTa                                <  1:3898878/71‑1 (MQ=255)
                                       ggTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCg                            >  1:3263078/1‑71 (MQ=255)
                                        gTTATCAAGATTGATGACATCATGACTGTTTTGCAGTa                                                            >  1:134538/1‑38 (MQ=37)
                                        gTTATCAAGAATGATGACATCATGACTGTTTTGCAGTaa                                                           >  1:4199931/1‑39 (MQ=255)
                                        gTTATCAAGAATGATGACATCATGACTGTTTTGCAGTaa                                                           >  1:2257974/1‑39 (MQ=255)
                                        gTTATCAAGAATGATGACATCATGACTGTTTTGCAGTaa                                                           >  1:3552511/1‑39 (MQ=255)
                                        gTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGc                           <  1:2176953/71‑1 (MQ=255)
                                        gTTATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGc                           <  1:1203390/71‑1 (MQ=255)
                                         ttATCAAGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGc                           <  1:2315565/70‑1 (MQ=255)
                                         ttATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGc                           >  1:3172022/1‑70 (MQ=255)
                                         ttATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCt                          <  1:375086/71‑1 (MQ=255)
                                          tATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTa                         >  1:3432403/1‑71 (MQ=255)
                                          tATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTa                         >  1:1372483/1‑71 (MQ=255)
                                              aaGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGt                                               >  1:4014418/1‑45 (MQ=255)
                                              aaGAATGATGACATCATGACTGTTTTGCAGTAATAGCACACAGGTATGACTTCCAATGTAACCGCTaccac                     >  1:1800696/1‑71 (MQ=255)
                                               aGAATGATGACATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCt                          <  1:1174550/65‑1 (MQ=255)
                                                gAATGATGACATCATGACCGTTTTGCAGTAATTGca                                                      >  1:2789229/1‑36 (MQ=255)
                                                gAATGATGACATCATGACCGTTTTGCAGTAATTGca                                                      >  1:2563964/1‑36 (MQ=255)
                                                gAATGATGACATCATGACCGTTTTGCAGTAATTGca                                                      >  1:2318644/1‑36 (MQ=255)
                                                   tgatgaCATCATGACTGTTTTGCAGTAATTGCACACAg                                                 <  1:262410/38‑1 (MQ=255)
                                                   tgatgaCATCATGACTGTTTTGCAGTAATTGCACACAg                                                 <  1:689298/38‑1 (MQ=255)
                                                   tgatgaCATCATGACTGTTTTGCAGTAATTGCACACAg                                                 <  1:2797090/38‑1 (MQ=255)
                                                     atgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                        >  1:2854356/1‑61 (MQ=255)
                                                     atgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                        >  1:2584455/1‑61 (MQ=255)
                                                     atgaCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTac                        >  1:3969833/1‑61 (MQ=255)
                                                      tgaCATCATGACTGTTTTGCAGTAATTGCACACAg                                                 <  1:582022/35‑1 (MQ=255)
                                                      tgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTa                                <  1:1509813/52‑1 (MQ=255)
                                                      tgaCATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAAc              >  1:3088543/1‑70 (MQ=255)
                                                        aCATCATGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAg           <  1:2034779/71‑1 (MQ=255)
                                                            catGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAAct       >  1:2900462/1‑71 (MQ=255)
                                                            catGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAAct       >  1:2743314/1‑71 (MQ=255)
                                                             atGACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCt                          <  1:3669126/51‑1 (MQ=255)
                                                             atGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActc      >  1:1114090/1‑71 (MQ=255)
                                                             atGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActc      >  1:130988/1‑71 (MQ=255)
                                                             atGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActc      >  1:677641/1‑71 (MQ=255)
                                                             atGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActc      >  1:4154197/1‑71 (MQ=255)
                                                               gACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActct     >  1:1059545/1‑70 (MQ=255)
                                                               gACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActct     >  1:2143130/1‑70 (MQ=255)
                                                               gACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActct     >  1:2941660/1‑70 (MQ=255)
                                                               gACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActct     >  1:309919/1‑70 (MQ=255)
                                                               gACTGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAActct     >  1:3600664/1‑70 (MQ=255)
                                                                 ccGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCAt  <  1:3207281/71‑1 (MQ=255)
                                                                  |                                                                     
GCTCGATAACAGGCAGTACGCTGCGCTTACTGTTACAGAGGTTATCAAGAATGATGACATCATGACCGTTTTGCAGTAATTGCACACAGGTATGACTTCCAATGTAACCGCTACCACCGGTAACCAGAACTCTCAT  >  minE/498375‑498510

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