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
A1 F21 I0 R2 308 27.9 1975068 96.7% 1909890 67.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 4,549,753 C→T 100% intergenic (+42/‑25) fimC → / → fimD chaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb4,549,7530CT91.7% 29.0 / ‑3.3 12intergenic (+42/‑25)fimC/fimDchaperone, periplasmic/outer membrane usher protein, type 1 fimbrial synthesis
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (3/8);  total (3/9)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACAC  >  W3110S.gb/4549683‑4549817
                                                                      |                                                                
cccccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGcc                                                                  <  1:1119767/71‑1 (MQ=255)
cccccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGcc                                                                  <  1:1673912/71‑1 (MQ=255)
cccccAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGcc                                                                  <  1:286009/71‑1 (MQ=255)
        aTGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCTGGGTGAtt                                                          >  1:1285478/1‑71 (MQ=255)
         tGAAGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCTGGGTGAttt                                                         >  1:403049/1‑71 (MQ=255)
                       gAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCAGGTGATTTTAAGCCGGAGGaat                                           <  1:1694401/71‑1 (MQ=255)
                        aaTAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCTGGGTGATTTTAAGCCGGAGGaata                                          <  1:1763043/71‑1 (MQ=255)
                        aaTAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCTGGGTGATTTTAAGCCGGAGGaata                                          <  1:22031/71‑1 (MQ=255)
                                aGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGcc                                                                  <  1:623614/39‑1 (MQ=255)
                                              gCCTGAATAAAAAGAATTGACTGCTGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGa                     <  1:613546/70‑1 (MQ=255)
                                              gCCTGAATAAAAAGAATTGACTGCTGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGa                     <  1:950819/70‑1 (MQ=255)
                                              gCCTGAATAAAAAGAATTGACTGCTGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGa                     <  1:993509/70‑1 (MQ=255)
                                                      aaaaaGAATTGACTGCTGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAg            >  1:1713273/1‑71 (MQ=255)
                                                                 aCTGCTGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacacac  <  1:486979/70‑1 (MQ=255)
                                                                 aCTGCTGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacacac  <  1:776797/70‑1 (MQ=255)
                                                                 aCTGCTGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAacacac  <  1:779624/70‑1 (MQ=255)
                                                                      |                                                                
CCCCCAAAATGACGGGCGTAATGGAATAACGCAGGGGGAATTTTTCGCCTGAATAAAAAGAATTGACTGCCGGGTGATTTTAAGCCGGAGGAATAATGTCATATCTGAATTTAAGACTTTACCAGCGAAACACAC  >  W3110S.gb/4549683‑4549817

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