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
A3 F2 I1 R1 2892 75.3 5698161 66.1% 3766484 59.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA Exported 608,981 T→C 21.2% I425V (ATC→GTC) ‡ pflB ← pyruvate formate lyase I

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*Exported608,9810TC21.2% 256.7 / 62.4 132I425V (ATC→GTC) ‡pflBpyruvate formate lyase I
Reads supporting (aligned to +/- strand):  ref base T (42/62);  new base C (15/13);  total (57/75)
Fisher's exact test for biased strand distribution p-value = 2.83e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 159 total aligned reads displayed.

TTGATTGCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTC  >  Exported/608911‑609051
                                                                      |                                                                      
  gATTGCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatc                                                                       <  1:2818379/70‑1 (MQ=255)
   aTTGCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatca                                                                      <  1:261160/70‑1 (MQ=255)
      gCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCgg                                                                  >  1:5340523/1‑71 (MQ=255)
           cAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                             >  1:2240311/1‑71 (MQ=255)
            aGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTAc                                                            <  1:196137/71‑1 (MQ=255)
              cATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                             <  1:4089256/68‑1 (MQ=255)
              cATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                             <  1:5202882/68‑1 (MQ=255)
              cATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACg                                                           >  1:2583007/1‑70 (MQ=255)
               aTGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                             >  1:3132667/1‑67 (MQ=255)
                tGGTTTTCGGCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACg                                                           <  1:4912499/68‑1 (MQ=255)
                tGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcag                                                        >  1:814231/1‑71 (MQ=255)
                tGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACAATCATCGGGCTTACg                                                           <  1:508464/68‑1 (MQ=255)
                 cgTTTTCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcag                                                        >  1:1143248/2‑70 (MQ=255)
                  gTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACgcagc                                                       <  1:1461504/70‑1 (MQ=255)
                   ttttCGCCAGGTTTGCACGCGCACCGATGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                             <  1:4923260/63‑1 (MQ=255)
                   ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatca                                                                      <  1:3517010/54‑1 (MQ=255)
                   ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatca                                                                      <  1:576990/54‑1 (MQ=255)
                   ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCtt                                                              <  1:1943784/62‑1 (MQ=255)
                   ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaa                                                     <  1:5109958/71‑1 (MQ=255)
                   ttttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaa                                                     <  1:4812571/71‑1 (MQ=255)
                    tttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatc                                                                       >  1:5134384/1‑52 (MQ=255)
                    tttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                    >  1:3055222/1‑71 (MQ=255)
                     ttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                    >  1:2391923/1‑70 (MQ=255)
                     ttCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaag                                                    >  1:2663018/1‑70 (MQ=255)
                      tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                               <  1:5587630/58‑1 (MQ=255)
                      tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                   <  1:2032018/70‑1 (MQ=255)
                      tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                   <  1:202592/70‑1 (MQ=255)
                      tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                   <  1:3043363/70‑1 (MQ=255)
                      tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                   <  1:5547664/70‑1 (MQ=255)
                      tCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                   <  1:5274704/70‑1 (MQ=255)
                      tCGCCAGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCagcaggc                                                   <  1:4334380/70‑1 (MQ=255)
                        gCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAgcaagcaa                                                 <  1:4224293/70‑1 (MQ=255)
                           aGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                             >  1:945354/1‑71 (MQ=255)
                           aGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                             >  1:2480333/1‑71 (MQ=255)
                           aGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                             >  1:4947648/1‑71 (MQ=255)
                           aGGTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGc                                             <  1:4923163/71‑1 (MQ=255)
                            ggTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatc                                                                       >  1:1341037/1‑44 (MQ=255)
                            ggTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatc                                                                       <  1:4240566/44‑1 (MQ=255)
                            ggTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                   >  1:4642752/1‑64 (MQ=255)
                            ggTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                            <  1:224252/71‑1 (MQ=255)
                             gTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCt                                                               <  1:4766030/51‑1 (MQ=255)
                             gTTAGCGCGTGCACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGt                                           <  1:2925223/71‑1 (MQ=255)
                              tttGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatcat                                                                     <  1:1834487/44‑1 (MQ=255)
                                 gCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatc                                                                       <  1:5612882/39‑1 (MQ=255)
                                 gCACGCGCACCGAAGAACTGCATTTGTTTACCAACGatc                                                                       <  1:2935523/39‑1 (MQ=255)
                                 gCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTa                                                             <  1:3726161/49‑1 (MQ=255)
                                 gCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACg                                                           >  1:3165380/1‑51 (MQ=255)
                                   aCGCGCACCGAAGAACTGCATTTGTTTACCAACGatcat                                                                     >  1:1657053/1‑39 (MQ=255)
                                   aCGCGCACCGAAGAACTGCATTTGTTTACCAACGatcat                                                                     >  1:4914727/1‑39 (MQ=255)
                                   aCGCGCACCGAAGAACTGCATTTGTTTACCAACGatca                                                                      <  1:252889/38‑1 (MQ=255)
                                     gcgcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCg                                   <  1:1110034/71‑1 (MQ=255)
                                       gcACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgtt                                 >  1:4528867/1‑71 (MQ=255)
                                       gcACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAgcaggcaa                                                 <  1:4796127/55‑1 (MQ=255)
                                        cACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                             <  1:4355125/58‑1 (MQ=255)
                                        cACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGc                                             <  1:3759162/58‑1 (MQ=255)
                                        cACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                <  1:2154030/71‑1 (MQ=255)
                                        cACCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAAtc                                               <  1:4774095/56‑2 (MQ=255)
                                         aCCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagc                                                       <  1:5172893/47‑1 (MQ=16)
                                         aCCAAAGAACTGCATTTGCTTACCAATCACCATTGGGCTGACgcagc                                                       <  1:2560571/47‑1 (MQ=16)
                                           caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCgctgtt                              >  1:514048/3‑70 (MQ=255)
                                           caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                             <  1:3782391/69‑1 (MQ=255)
                                           caaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                             <  1:5360228/69‑1 (MQ=255)
                                           cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCg                                            <  1:192719/56‑1 (MQ=255)
                                           cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                             <  1:3985486/71‑1 (MQ=255)
                                           cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                             <  1:4459885/71‑1 (MQ=255)
                                           cGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                             <  1:2209975/71‑1 (MQ=255)
                                            gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACgcagca                                                      >  1:4493100/1‑45 (MQ=255)
                                            gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACgcagca                                                      >  1:2836770/1‑45 (MQ=255)
                                            gaagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGa                            <  1:217997/71‑1 (MQ=255)
                                            aaagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGctgttg                             >  1:1616873/2‑70 (MQ=255)
                                             aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATa                                               >  1:4730602/1‑51 (MQ=255)
                                             aagaaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGttgttg                             >  1:4654861/1‑69 (MQ=255)
                                             aagaaCTGCATTTGCTTACCAATCACCATTGGGCTGACgcagc                                                       >  1:1492323/1‑43 (MQ=16)
                                              agaaCTGCATTTGTTTACCAACGATCATCGGGCtt                                                              <  1:3276428/35‑1 (MQ=255)
                                              agaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCagcaggc                                                   <  1:3828394/46‑1 (MQ=16)
                                              agaaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCagcaggc                                                   <  1:3829407/46‑1 (MQ=16)
                                                aaCTGCATTTGTTTACCAACGATCATCGGGCTTACGCagcaagc                                                   <  1:5574477/44‑1 (MQ=255)
                                                aaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAAtcgtcgc                                  <  1:3580464/61‑2 (MQ=255)
                                                aaCTGCATTTGCTTACCAATCACCATTGGGCTGACGCAGCAGGCAATCGCGTAATCGTCGCTGTTGAAGTc                        <  1:1569837/71‑1 (MQ=255)
                                                  cTGCATTTGTTTACCAACGATCATCGGGCTTACGCAgcaagcaa                                                 >  1:5648645/1‑44 (MQ=255)
                                                   tGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTc                                       <  1:762743/53‑1 (MQ=255)
                                                    gCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAAt                                                >  1:1195933/1‑43 (MQ=255)
                                                       tttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATa                                               <  1:2369170/41‑1 (MQ=255)
                                                        ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTc                                       <  1:3881398/48‑1 (MQ=255)
                                                        ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                      <  1:5176578/65‑1 (MQ=255)
                                                        ttGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCg                      <  1:659474/65‑1 (MQ=255)
                                                          gTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGa                    >  1:5244188/1‑65 (MQ=255)
                                                           tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCgttg                                <  1:172749/52‑1 (MQ=255)
                                                           tttACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCAt               >  1:4548540/1‑69 (MQ=255)
                                                              aCCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAgg           <  1:3253912/70‑1 (MQ=255)
                                                               ccAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGt          <  1:1329495/70‑1 (MQ=255)
                                                                 aaCGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCAt       <  1:2096741/71‑1 (MQ=255)
                                                                   cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg     >  1:822877/1‑71 (MQ=255)
                                                                   cGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCg     <  1:4051844/71‑1 (MQ=255)
                                                                    gATCATCGGTCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGt    >  1:3346541/1‑71 (MQ=255)
                                                                      tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc         >  1:1007848/1‑64 (MQ=255)
                                                                      tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc         >  1:4006540/1‑64 (MQ=255)
                                                                      tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTc         >  1:1557215/1‑64 (MQ=255)
                                                                      tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtc  <  1:3016969/71‑1 (MQ=255)
                                                                      tcatcGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTtc  <  1:2113837/71‑1 (MQ=255)
                                                                      |                                                                      
TTGATTGCGTACAGCATGGTTTTCGCCAGGTTTGCACGCGCACCGAAGAACTGCATTTGTTTACCAACGATCATCGGGCTTACGCAGCAAGCAATAGCGTAGTCATCGTTGTTGAAGTCCGGACGCATCAGGTCATCGTTC  >  Exported/608911‑609051

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