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 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,827,240 |
T→G |
55.2% |
A161A (GCT→GCG) |
mutS → |
methyl‑directed mismatch repair protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,827,240 | 0 | T | G | 55.2%
| 21.5
/ 54.9
| 58 | A161A (GCT→GCG) | mutS | methyl‑directed mismatch repair protein |
| Reads supporting (aligned to +/- strand): ref base T (13/13); new base G (18/14); total (31/27) |
| Fisher's exact test for biased strand distribution p-value = 7.92e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.16e-01 |
ACAGCAAAGGTTTCGGCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAACTGCTGTA > minE/1827173‑1827296
|
aCAGCAAAGGTTTCGGCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTg > 1:132312/1‑69 (MQ=255)
aCAGCAAAGGTTTCGGCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTg > 1:2267202/1‑69 (MQ=255)
aCAGCAAAGGTTTCGGCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTg > 1:192207/1‑69 (MQ=255)
ggCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGAt < 1:128779/68‑1 (MQ=255)
ggCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGAt < 1:2093320/68‑1 (MQ=255)
ggCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGAt < 1:2056583/68‑1 (MQ=255)
ggCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGAt < 1:2219390/68‑1 (MQ=255)
tACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATggc > 1:2706250/1‑68 (MQ=255)
tACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATggc > 1:16355/1‑68 (MQ=255)
cgACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAg < 1:2764869/69‑1 (MQ=255)
cgACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAg < 1:2022611/69‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGCGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:1318287/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGCACCGGCGGACCGCGaa > 1:429991/2‑55 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGGGAAACGATGGCGGCAGa > 1:3154256/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAg > 1:840002/2‑68 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:2739237/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:2700958/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:2647188/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:308852/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:826976/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:3018624/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:3033091/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:2313989/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:3324490/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:3359621/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:3397973/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:618943/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:75983/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:808233/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:252880/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:1197305/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:1102612/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:1579637/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:1625169/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:1728403/68‑1 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:2115066/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:2159713/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:2174639/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:910358/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:2585861/2‑69 (MQ=255)
aaCGCTGGATATCAGTTCCGGTCGTTTTCGCATGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa > 1:3009112/2‑69 (MQ=255)
aaCGCTGGATATCACTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGAAACGATGGCGGCAGa < 1:3267556/68‑1 (MQ=255)
aaCGCTCGATATCAGTTCCGGTCGTTTTCGCCTGAGCGAACCGGCGGACCGCGaaa > 1:438637/2‑56 (MQ=255)
cTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACt > 1:2164915/1‑68 (MQ=255)
cTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACt > 1:930819/1‑68 (MQ=255)
cTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACt > 1:2312400/1‑68 (MQ=255)
cTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACt > 1:1370106/1‑68 (MQ=255)
ttCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTaa < 1:1908359/69‑1 (MQ=255)
ttCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTaa < 1:412604/69‑1 (MQ=255)
ttCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTaa < 1:658397/69‑1 (MQ=255)
ccGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATc > 1:1991866/1‑69 (MQ=255)
cGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGc > 1:625788/1‑68 (MQ=255)
ttCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAAc < 1:98919/69‑1 (MQ=255)
ttCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAAc < 1:2587818/69‑1 (MQ=255)
ttCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAAc < 1:2254780/69‑1 (MQ=255)
ttCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAAc > 1:1347957/1‑69 (MQ=255)
aGCGAACCGGCTGACCGCGAAACGATGGCGCCAGAACTGCAACGCACTAATCCTGCGGAACTGCTGTa < 1:294703/68‑1 (MQ=255)
gCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAACTGCTGt > 1:1796693/1‑66 (MQ=255)
|
ACAGCAAAGGTTTCGGCTACGCGACGCTGGATATCAGTTCCGGGCGTTTTCGCCTGAGCGAACCGGCTGACCGCGAAACGATGGCGGCAGAACTGCAACGCACTAATCCTGCGGAACTGCTGTA > minE/1827173‑1827296
|
| 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
