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 4,328,660 C→T 13.5% V125I (GTC→ATC)  phnD ← phosphonate/organophosphate ester transporter subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,328,6600CT13.5% 165.2 / 13.7 59V125I (GTC→ATC) phnDphosphonate/organophosphate ester transporter subunit
Reads supporting (aligned to +/- strand):  ref base C (26/25);  new base T (6/2);  total (32/27)
Fisher's exact test for biased strand distribution p-value = 2.69e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.86e-01

TTGCCAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGG  >  W3110S.gb/4328590‑4328728
                                                                      |                                                                    
ttGCCAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGAc                                                                      >  1:4124366/1‑71 (MQ=255)
     aaaGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATc                                                                  >  1:1304035/1‑70 (MQ=255)
        ggTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAaca                                                              >  1:4387421/1‑71 (MQ=255)
        ggTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAaca                                                              >  1:2149417/1‑71 (MQ=255)
         gTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAacac                                                             >  1:365446/1‑71 (MQ=255)
            agaTCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGc                                                           <  1:1333581/70‑1 (MQ=255)
            agaTCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCt                                                          >  1:1507087/1‑71 (MQ=255)
            agaTCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCt                                                          >  1:2090796/1‑71 (MQ=255)
                cTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCGAg                                                      >  1:1478105/1‑71 (MQ=255)
                cTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAg                                                      >  1:4548090/1‑71 (MQ=255)
                cTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAg                                                      >  1:3139489/1‑71 (MQ=255)
                   tCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTaa                                                   >  1:3382766/1‑71 (MQ=255)
                   tCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCa                                                       <  1:1813743/67‑1 (MQ=255)
                   tCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGt                                                     <  1:1288028/69‑1 (MQ=255)
                   tCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTaa                                                   >  1:4002605/1‑71 (MQ=255)
                   tCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTaa                                                   >  1:3042994/1‑71 (MQ=255)
                     cGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAAcc                                                 >  1:4409334/1‑71 (MQ=255)
                        ttCGCCAGCAGATCGTTCAGGTTGTTGATCGGAGTGTCTTTGTTGACGATCAACACGCTCCAGTAAc                                                  >  1:360653/1‑67 (MQ=255)
                          cGCCAGCAGATCGTTCAGGGTGTTGATCGGACTGTCTTTGTTGACGATCCACACGCTCCAGTAACCCgg                                              <  1:1668282/69‑1 (MQ=255)
                           gCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCg                                            <  1:1543889/70‑1 (MQ=255)
                           gCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGa                                           <  1:1816068/71‑1 (MQ=255)
                              agcagATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGat                                          >  1:3525597/1‑69 (MQ=255)
                              agcagATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatcc                                        <  1:4374467/71‑1 (MQ=255)
                               gcagATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCa                                                                 <  1:4001899/45‑1 (MQ=255)
                               gcagATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatcca                                       <  1:3541070/71‑1 (MQ=255)
                                 agATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatccatc                                     >  1:3978701/1‑71 (MQ=255)
                                  gATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatccatc                                     >  1:3375807/1‑70 (MQ=255)
                                  gATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatccatc                                     >  1:1418856/1‑70 (MQ=255)
                                  gATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatcca                                       >  1:4020322/1‑68 (MQ=255)
                                   aTCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATccg                                   >  1:406671/1‑71 (MQ=255)
                                    tCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATctgc                                  <  1:1748614/71‑1 (MQ=255)
                                       ttCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTcc                                                        <  1:3556036/46‑1 (MQ=255)
                                        tCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATccg                                   >  1:2940651/1‑66 (MQ=255)
                                         cAGGTTGTTGATCGGACTGTCTTTGTTGACGATCaa                                                                >  1:2068184/1‑36 (MQ=255)
                                         cAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCcgcg                              <  1:3525188/70‑1 (MQ=255)
                                         cAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGa                             >  1:3133478/1‑71 (MQ=255)
                                                 tgATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTgg                     >  1:2297984/1‑71 (MQ=255)
                                                 tgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCgg                                              >  1:3738721/1‑46 (MQ=255)
                                                  gATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGatcca                                       <  1:3822904/52‑1 (MQ=255)
                                                   aTCGGACTGTCTTTGTTGACGATCAACACGCTCGAGTAACCCGGCGATCCATCCGCCGCGACCGTCTgg                     <  1:2536281/69‑1 (MQ=255)
                                                   aTCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGc                   >  1:3272231/1‑71 (MQ=255)
                                                    tCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCg                  <  1:26244/71‑1 (MQ=255)
                                                    tCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGGCTGGGCg                  <  1:2850416/71‑1 (MQ=255)
                                                     cGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGc                                             >  1:2347984/1‑43 (MQ=255)
                                                      ggACTGTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCg                  >  1:3959671/1‑69 (MQ=255)
                                                       gACTGTCTTTGTTGACGATCAACACGCTCCAGTAAcc                                                 <  1:3736645/37‑1 (MQ=255)
                                                       gACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGAcc                           <  1:1760167/59‑1 (MQ=255)
                                                          tGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCg                          <  1:743626/57‑1 (MQ=255)
                                                            tCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGAcc            <  1:2071612/69‑1 (MQ=255)
                                                            tCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGAcc            <  1:4173056/69‑1 (MQ=255)
                                                            tCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTg          <  1:4493859/71‑1 (MQ=255)
                                                             cTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTgg         >  1:811881/1‑71 (MQ=255)
                                                              tttGTTGACGATCAACACGCTCCAGTAACCCGGCGatccatc                                     >  1:3547589/1‑42 (MQ=255)
                                                              tttGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAg               <  1:3790615/64‑1 (MQ=255)
                                                               ttgttgACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGc        >  1:4290235/1‑70 (MQ=255)
                                                                tgttgACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGcc       <  1:2593741/70‑1 (MQ=255)
                                                                  ttgACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCAt     <  1:287404/70‑1 (MQ=255)
                                                                    gACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGt                         <  1:1746826/48‑1 (MQ=255)
                                                                     aCGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCg                  >  1:3850428/1‑54 (MQ=255)
                                                                     aCGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTgg  <  1:320378/70‑1 (MQ=255)
                                                                      |                                                                    
TTGCCAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTGG  >  W3110S.gb/4328590‑4328728

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A