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 F28 I1 R2 146 74.7 3299319 84.8% 2797822 66.9

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA minE 1,827,842 Δ1 bp coding (1085/2562 nt) mutS → methyl‑directed mismatch repair protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,827,8400C.93.3% 51.0 / ‑0.9 15coding (1083/2562 nt)mutSmethyl‑directed mismatch repair protein
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base . (14/0);  total (15/0)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.63e-01

TCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGT  >  minE/1827791‑1827901
                                                 |                                                             
tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                         >  1:2047896/1‑71 (MQ=255)
tCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCG‑CCACGCGATCTGGCCCGTATgc                                         >  1:762733/1‑71 (MQ=255)
                                        aaCTGCTCGCCC‑CGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAg   >  1:390990/1‑69 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAg   >  1:1472349/1‑69 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:1578432/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:1705539/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:1826484/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:1864867/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:1919125/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:2182725/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:2413620/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:2722337/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:3099887/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:712034/1‑70 (MQ=255)
                                        aaCTGCTCG‑CCACGCGATCTGGCCCGTATGCGCCACGCCTTCCAGCAACTGCCGGAGCTGCGTGCGCAGt  >  1:1846657/1‑70 (MQ=255)
                                                 |                                                             
TCGGCGACCTGGAACGTATTCTGGCACGTCTGGCTTTACGAACTGCTCGCCCACGCGATCTGGCCCGTATGCGCCACGCTTTCCAGCAACTGCCGGAGCTGCGTGCGCAGT  >  minE/1827791‑1827901

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