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
A2 F17 I0 R1 71 95.7 2922988 91.7% 2680379 65.6

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,361,309:1 +C 100% coding (1071/1110 nt) mrp ← antiporter inner membrane protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,361,3091.C94.4% 57.8 / ‑2.5 18coding (1071/1110 nt)mrpantiporter inner membrane protein
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (17/0);  total (17/1)
Fisher's exact test for biased strand distribution p-value = 5.56e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.
Rejected as polymorphism: Polymorphic indel expands or contracts a homopolymer stretch.

GTTAGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCA‑CCCTGCCAGTAGAGCTGAGCTGCAACGCGGT  >  minE/1361269‑1361340
                                         |                               
gTTAGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCA‑CCCTGCCAGTAGAGCTGAGCTGCAAcgcg    <  1:1995113/70‑1 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1976576/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:783423/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:699795/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:399481/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:2848648/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:2679896/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:224354/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1983933/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1172957/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1870126/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1838682/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1775236/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1533781/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1505382/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1317106/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1308810/1‑70 (MQ=255)
   aGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCACCCCTGCCAGTAGAGCTGAGCTGCAACGCGGt  >  1:1305006/1‑70 (MQ=255)
                                         |                               
GTTAGACCGCGCGGAAGGAAATCTCGCCTGGAATGACTTCA‑CCCTGCCAGTAGAGCTGAGCTGCAACGCGGT  >  minE/1361269‑1361340

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