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 F28 I2 R2 154 32.4 3140800 76.4% 2399571 54.5

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA W3110S.gb 2,581,399 G→A A12V (GCT→GTT)  ypfG ← hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb2,581,3990GA90.9% 58.7 / ‑1.1 22A12V (GCT→GTT) ypfGhypothetical protein
Reads supporting (aligned to +/- strand):  ref base G (2/0);  new base A (0/20);  total (2/20)
Fisher's exact test for biased strand distribution p-value = 4.33e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.91e-01

AAGACGTCGGCAACAAAGCGAAAAAAAAGAGAAGGAAAATGCGATAGCGCATGGACGGTACGACCCCAGAAG  >  W3110S.gb/2581382‑2581453
                 |                                                      
aaGACATCGGCAACAAAACG‑AAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:491684/62‑1 (MQ=37)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1226268/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:2896621/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:2536119/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1909375/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1890780/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1866834/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1715320/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1590977/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1545547/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1348092/62‑1 (MQ=255)
 aGACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1092652/62‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:1627539/61‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:2016349/61‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:2444376/61‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:2521464/61‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:482542/61‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:72637/61‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:759180/61‑1 (MQ=255)
  gACATCGGCAACAAAACGAAAAAAAAGAGAAGGAAAATGCGATATCGCATGGACGGTACGa           <  1:82105/61‑1 (MQ=255)
          caacaaAGCGAAAAAAAAGAGAAGGAAAATGCGATAGCGCATGGACGGTACGACCCCAGaa   >  1:1309465/1‑61 (MQ=255)
          caacaaAGCGAAAAAAAAGAGAAGGAAAATGCGATAGCGCATGGACGGTACGACCCCAGAAg  >  1:1468710/1‑62 (MQ=255)
                 |                                                      
AAGACGTCGGCAACAAAGCGAAAAAAAAGAGAAGGAAAATGCGATAGCGCATGGACGGTACGACCCCAGAAG  >  W3110S.gb/2581382‑2581453

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