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
A6 F28 I1 R2 90 19.5 1203533 67.3% 809977 57.3

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 1,470,362 +C coding (1360/3753 nt) yfaL ← adhesin

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,470,3581.C94.1% 54.3 / ‑2.6 17coding (1364/3753 nt)yfaLadhesin
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (0/16);  total (0/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.36e-01

TATATCGCCGGTTAGCGCCATCGACTGCG‑CCCCTGCCAGCACGTAGCTGCCGTTTTGCGCAA  >  minE/1470330‑1470391
                             |                                 
tataTCGCCGGTTAGCGCCATCGACTGCG‑CCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:1004396/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:161370/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:90679/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:631423/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:545667/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:524948/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:511515/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:494281/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:474495/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:325209/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:150411/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:138915/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:128105/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:1135465/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:1005767/62‑1 (MQ=255)
 atatCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:1005581/62‑1 (MQ=255)
    tCGCCGGTTAGCGCCATCGACTGCGCCCCCTGCCAGCACGTAGCTGCCGTTTTGCGCaa  <  1:134999/59‑1 (MQ=255)
                             |                                 
TATATCGCCGGTTAGCGCCATCGACTGCG‑CCCCTGCCAGCACGTAGCTGCCGTTTTGCGCAA  >  minE/1470330‑1470391

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