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 F21 I0 R2 316 65.6 5147759 97.4% 5013917 60.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 3,263,996 C→T 43.3% V293M (GTG→ATG)  tdcC ← L‑threonine/L‑serine transporter

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb3,263,9960CT43.3% 28.6 / 75.0 60V293M (GTG→ATG) tdcCL‑threonine/L‑serine transporter
Reads supporting (aligned to +/- strand):  ref base C (19/15);  new base T (8/18);  total (27/33)
Fisher's exact test for biased strand distribution p-value = 6.92e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

AGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTAAAGGCAAAG  >  W3110S.gb/3263929‑3264066
                                                                   |                                                                      
aGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTgg                                                                     <  1:802606/71‑1 (MQ=255)
aGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTgg                                                                     <  1:1615923/71‑1 (MQ=255)
  tgtAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGaa                                                                   >  1:297337/1‑71 (MQ=255)
  tgtAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGaa                                                                   <  1:909372/71‑1 (MQ=255)
   gtAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGaa                                                                   >  1:2355335/1‑70 (MQ=255)
   gtAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGaa                                                                   >  1:352231/1‑70 (MQ=255)
    tAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAata                                                                 >  1:4136683/1‑71 (MQ=255)
    tAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAata                                                                 >  1:1075690/1‑71 (MQ=255)
         gcgAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAat                                                                  >  1:2456915/1‑65 (MQ=255)
             aCGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCt                                                        >  1:2346806/1‑71 (MQ=255)
               gttgttTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAatat                                                                <  1:217371/61‑1 (MQ=255)
                 tgttTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTgg                                                    >  1:2464443/1‑71 (MQ=255)
                  gttTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGc                                                   >  1:4968789/1‑71 (MQ=255)
                  gttTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGc                                                   >  1:1449688/1‑71 (MQ=255)
                   ttttGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCtt                                                       <  1:2865799/66‑1 (MQ=255)
                        gTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGc                                             <  1:2947384/71‑1 (MQ=255)
                         tACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGcc                                            <  1:673408/71‑1 (MQ=255)
                           ccGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCAt                                          <  1:4508279/71‑1 (MQ=255)
                           ccGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCAt                                          <  1:677627/71‑1 (MQ=255)
                              gTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCt                                                        <  1:2472262/54‑1 (MQ=255)
                              gTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGtt                                       <  1:3352467/71‑1 (MQ=255)
                              gTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGtt                                       <  1:342960/71‑1 (MQ=255)
                               tCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGt                                        >  1:4824337/1‑69 (MQ=255)
                               tCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTg                                      <  1:2535169/71‑1 (MQ=255)
                                cATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCtt                                                       >  1:4091394/1‑53 (MQ=255)
                                  tGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTgcg                                                          <  1:4583880/48‑1 (MQ=255)
                                  tGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTgcg                                                          <  1:3166717/48‑1 (MQ=255)
                                  tGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCttt                                                      <  1:4377731/52‑1 (MQ=255)
                                   ggACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCg                                  >  1:4273361/1‑71 (MQ=255)
                                   ggACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCg                                  >  1:335988/1‑71 (MQ=255)
                                    gACGCAAAGTGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCAt                                          <  1:4608344/62‑1 (MQ=255)
                                    gACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCt                                                  >  1:2986345/1‑54 (MQ=255)
                                            gTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACagag                         >  1:2875612/1‑71 (MQ=255)
                                             tGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGt                        <  1:2180680/71‑1 (MQ=255)
                                             tGGTTAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGt                        <  1:4336706/71‑1 (MQ=255)
                                               gTTAGCCAGATAAGAAAGCACTGGAATATTCTgcgc                                                         <  1:505508/36‑1 (MQ=255)
                                                ttAGCCAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGc                                             >  1:2500857/1‑47 (MQ=255)
                                                   gCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACa                   <  1:2892251/70‑1 (MQ=255)
                                                     cAGATAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACa                            <  1:3415439/59‑1 (MQ=255)
                                                     cAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAgg                 >  1:349536/1‑70 (MQ=255)
                                                        aTAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGgag                               <  1:5066992/53‑1 (MQ=255)
                                                        aTAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTaa                      >  1:2671990/1‑62 (MQ=255)
                                                        aTAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTaa                      >  1:742974/1‑62 (MQ=255)
                                                         tAAGAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCt            <  1:297713/71‑1 (MQ=255)
                                                         tAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCt            <  1:2726959/71‑1 (MQ=255)
                                                         tAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCt            <  1:561064/71‑1 (MQ=255)
                                                          aaGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGga                                <  1:715971/50‑1 (MQ=255)
                                                          aaGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTaaa                     >  1:446587/1‑61 (MQ=255)
                                                          aaGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTaaa                     >  1:86157/1‑61 (MQ=255)
                                                           aGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTa           <  1:3913673/70‑1 (MQ=255)
                                                            gAAAGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTaa          <  1:2785519/70‑1 (MQ=255)
                                                            gAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTaaa         <  1:1226968/71‑1 (MQ=255)
                                                               aGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTAAAGGc      <  1:4307244/71‑1 (MQ=255)
                                                               aGCATTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTAAAGGc      <  1:2413839/71‑1 (MQ=255)
                                                               aGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTAAAgg       >  1:1740192/1‑70 (MQ=255)
                                                                gCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGtt                                       >  1:4600859/1‑37 (MQ=255)
                                                                gCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGtt                                       >  1:4258420/1‑37 (MQ=255)
                                                                gCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGtt                                       >  1:2745148/1‑37 (MQ=255)
                                                                gCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGtt                                       >  1:1371962/1‑37 (MQ=255)
                                                                gCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTAAAGGCa     <  1:2748151/71‑1 (MQ=255)
                                                                   cTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTAAAGGCAAAg  <  1:699646/71‑1 (MQ=255)
                                                                   |                                                                      
AGTGTAATCGCGAACGTTGTTTTGGTACCGGTCATGGACGCAAAGTGGTTAGCCAGATAAGAAAGCACTGGAATATTCTGCGCTTTGGCTTCCGCCATGTTGGCCGGAGACAGAGTAAACAGGCAGCTAAAGGCAAAG  >  W3110S.gb/3263929‑3264066

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