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
A5 F17 I0 R2 162 60.6 4616657 98.5% 4547407 62.1

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,741,050 G→A 16.4% G326D (GGC→GAC)  yieG → predicted inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,741,0500GA16.4% 204.7 / 27.7 79G326D (GGC→GAC) yieGpredicted inner membrane protein
Reads supporting (aligned to +/- strand):  ref base G (37/29);  new base A (8/5);  total (45/34)
Fisher's exact test for biased strand distribution p-value = 7.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGACCGGTTCGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTCGCCGCT  >  W3110S.gb/3740981‑3741119
                                                                     |                                                                     
tGACCGGTTCGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTgg                                                                       <  1:1140214/70‑1 (MQ=255)
 gACCGGTTCGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTATTCCGGCGTATCGGTTGGCg                                                                     >  1:337766/1‑71 (MQ=255)
    cGGTTCGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTc                                                                  >  1:1253156/1‑71 (MQ=255)
        tCGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTAc                                                              >  1:2976096/1‑71 (MQ=255)
         cGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTAc                                                              <  1:446058/70‑1 (MQ=255)
         cGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTAc                                                              <  1:2145695/70‑1 (MQ=255)
          gTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCg                                                            >  1:1893323/1‑71 (MQ=255)
          gTTTATCGGTACTTCTTACGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTAcc                                                             <  1:1198398/70‑1 (MQ=255)
             tATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTa                                                               >  1:1567311/1‑65 (MQ=255)
             tATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTc                                                         >  1:770424/1‑71 (MQ=255)
             tATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTc                                                         >  1:4518960/1‑71 (MQ=255)
             tATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTc                                                         >  1:3706941/1‑71 (MQ=255)
             tATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTc                                                         >  1:429142/1‑71 (MQ=255)
               tCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCt                                                        <  1:3070138/70‑1 (MQ=255)
                cGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGACGGTCGTACCGGTCTGa                                                      >  1:1904672/1‑71 (MQ=255)
                 ggTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGAc                                                     <  1:3715074/71‑1 (MQ=255)
                  gTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGGTGGCGGTCGTACCGGTCTGAc                                                     <  1:4529574/70‑1 (MQ=255)
                    aCTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGACGGTCGTACCGGTCTGACgg                                                   >  1:1512772/1‑70 (MQ=255)
                    aCTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGACGGTCGTACCGGTCTGACgg                                                   >  1:64396/1‑70 (MQ=255)
                       tcttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGt                                               >  1:3901386/1‑71 (MQ=255)
                       tcttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGACGGTCGTACCGGTCTGACGGCAGt                                               >  1:1960070/1‑71 (MQ=255)
                        cttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTgg                                                                       >  1:2550946/1‑46 (MQ=255)
                        cttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTAc                                                              <  1:4195011/55‑1 (MQ=255)
                        cttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGa                                                      >  1:2951450/1‑63 (MQ=255)
                        cttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAg                                                <  1:2592602/69‑1 (MQ=255)
                        cttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGt                                               <  1:4086034/70‑1 (MQ=255)
                        cttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGt                                               >  1:3333547/1‑70 (MQ=255)
                        cttcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTg                                              >  1:2607529/1‑71 (MQ=255)
                          tcCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCg                                                            >  1:1509277/1‑55 (MQ=255)
                           ccGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTg                                              <  1:4164425/68‑1 (MQ=255)
                           ccGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGGCGTACCGGTCTGACGGCAGTg                                              <  1:3281634/68‑1 (MQ=255)
                           ccGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGACGGTCGTACCGGTCTGACGGCAGTGgt                                            <  1:2242557/70‑1 (MQ=255)
                            cGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGgttg                                          >  1:272178/1‑71 (MQ=255)
                            cGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGgtt                                           <  1:3018435/70‑1 (MQ=255)
                              ttACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGgttgt                                         <  1:1945785/70‑1 (MQ=255)
                                aCGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGttgttg                                       <  1:3707734/70‑1 (MQ=255)
                                aCGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTgg                                      >  1:3404648/1‑71 (MQ=255)
                                aCGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTgg                                      >  1:4533932/1‑71 (MQ=255)
                                aCGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTgg                                      >  1:2715466/1‑71 (MQ=255)
                                  ggCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTc                                    >  1:3508861/1‑71 (MQ=255)
                                  ggCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGACGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTc                                    >  1:2508810/1‑71 (MQ=255)
                                   gCTTATATTGAGTCCTATTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTct                                   >  1:2157001/1‑71 (MQ=255)
                                      tataTTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTctgct                                >  1:826742/1‑71 (MQ=255)
                                      tataTTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTAACGGCAGTGGttgttg                                       >  1:3402054/1‑64 (MQ=255)
                                       atatTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGt                                                                <  1:335602/38‑1 (MQ=255)
                                       atatTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAg                                                >  1:3147365/1‑54 (MQ=255)
                                       atatTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTctgctg                               >  1:3229226/1‑71 (MQ=255)
                                       atatTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTctgctg                               >  1:4361337/1‑71 (MQ=255)
                                       atatTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTctgc                                 <  1:3880813/69‑1 (MQ=255)
                                        tatTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTg                                                       >  1:848593/1‑46 (MQ=255)
                                        tatTGAGTCCTCTTCCGGCGTATCGGTTGACGGTCGTACCGGTCTGa                                                      >  1:1172345/1‑47 (MQ=255)
                                           tGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGttgttg                                       >  1:1719815/1‑59 (MQ=255)
                                                  tctTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGtt                             <  1:312428/62‑1 (MQ=255)
                                                   ctTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGgttg                                          >  1:1087281/1‑48 (MQ=255)
                                                    ttCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTgg                     >  1:425062/1‑68 (MQ=255)
                                                    ttCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTa                  >  1:411268/1‑71 (MQ=255)
                                                      ccGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGt                                     >  1:1195388/1‑50 (MQ=255)
                                                      ccGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCct                          <  1:4316213/61‑1 (MQ=255)
                                                      ccGGCGTATCGGTTGACGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGtt                   <  1:2233297/68‑1 (MQ=255)
                                                       cGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCt               <  1:1802616/71‑1 (MQ=255)
                                                       cGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCt               <  1:366153/71‑1 (MQ=255)
                                                        ggCGTATCGGTTGGCGGTCGTACCGGTCTGACGGc                                                  <  1:2753639/35‑1 (MQ=255)
                                                         gCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCttt             <  1:4208226/71‑1 (MQ=255)
                                                         gCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCttt             <  1:2369344/71‑1 (MQ=255)
                                                         gCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCttt             <  1:478365/71‑1 (MQ=255)
                                                         gCGTATCGGTTGACGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCttt             <  1:3500213/71‑1 (MQ=255)
                                                            tATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCctgct                       <  1:871027/58‑1 (MQ=255)
                                                            tATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCctgct                       <  1:1913951/58‑1 (MQ=255)
                                                             aTCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGt         >  1:1924547/1‑71 (MQ=255)
                                                             aTCGGTTGACGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGt         >  1:4593413/1‑71 (MQ=255)
                                                              tCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGgttgt                                         <  1:12472/38‑1 (MQ=255)
                                                              tCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGgttgt                                         <  1:2395210/38‑1 (MQ=255)
                                                              tCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGt         >  1:2922669/1‑70 (MQ=255)
                                                              tCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTc        >  1:4379589/1‑71 (MQ=255)
                                                              tCGGTTGACGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGt         <  1:4548763/70‑1 (MQ=255)
                                                                ggTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTcg       <  1:3523880/70‑1 (MQ=255)
                                                                ggTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTcg       >  1:392262/1‑70 (MQ=255)
                                                                ggTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTcg       >  1:4167775/1‑70 (MQ=255)
                                                                ggTTGACGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGt         >  1:4606254/1‑68 (MQ=255)
                                                                 gTTGACGGTCGTACCGGTCTGACGGCAGTGGttgttg                                       <  1:1412912/37‑1 (MQ=255)
                                                                   tGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTcgccgc   >  1:1637727/1‑71 (MQ=255)
                                                                    ggCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTCGCCGCt  >  1:384417/1‑71 (MQ=255)
                                                                     |                                                                     
TGACCGGTTCGTTTATCGGTACTTCTTCCGTTACGGCTTATATTGAGTCCTCTTCCGGCGTATCGGTTGGCGGTCGTACCGGTCTGACGGCAGTGGTTGTTGGTCTGCTGTTCCTGCTGGTTATCTTTCTGTCGCCGCT  >  W3110S.gb/3740981‑3741119

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A