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 |
2,183,975 |
T→C |
22.3% |
G1417G (GGT→GGC) |
gltB → |
glutamate synthase, large subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,183,975 | 0 | T | C | 22.3%
| 74.1
/ 15.9
| 58 | G1417G (GGT→GGC) | gltB | glutamate synthase, large subunit |
| Reads supporting (aligned to +/- strand): ref base T (41/4); new base C (9/4); total (50/8) |
| Fisher's exact test for biased strand distribution p-value = 6.60e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
AACGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTAA > minE/2183910‑2184040
|
taCGGTTGTGAAGATATGACGGGTGGTATCGTCTGCATTCTCGGTAAAACCGGCGTTAACTTCGGTGc > 1:2373891/2‑68 (MQ=255)
aaCGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCg > 1:2607993/1‑69 (MQ=255)
aaCGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCg > 1:1198211/1‑69 (MQ=255)
aaCGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCg > 1:2236468/1‑69 (MQ=255)
aCGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCg > 1:724972/1‑68 (MQ=255)
aCGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCg > 1:3002235/1‑68 (MQ=255)
aCGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCg > 1:2032365/1‑68 (MQ=255)
aCGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCg > 1:1599739/1‑68 (MQ=255)
ggTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGc < 1:981496/69‑1 (MQ=255)
tgtgAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATg > 1:1322097/1‑69 (MQ=255)
gtggtATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCtt > 1:1462166/1‑69 (MQ=255)
tggtATCGTCTGCATTCTGGGTAAAAGCGGCGTTAACTACGGTGCGGGCATGACCGGCGGTTTCGCTTa > 1:2004502/1‑69 (MQ=255)
tggtATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTa > 1:668938/1‑69 (MQ=255)
tCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGtt > 1:1377704/1‑68 (MQ=255)
tCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtc > 1:1116383/1‑69 (MQ=255)
tCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtc > 1:539861/1‑69 (MQ=255)
tCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtc > 1:18809/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:2559771/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:2454631/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:2713262/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:3277690/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:408952/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:1950041/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:1093396/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:151409/1‑69 (MQ=255)
gTCTGCATTCTGGGTAAAACCGGAGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTtctc > 1:1594196/1‑69 (MQ=255)
tGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGAt < 1:63892/69‑1 (MQ=255)
tGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGAt < 1:11433/69‑1 (MQ=255)
cTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAgc > 1:528176/1‑69 (MQ=255)
cTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAgc > 1:812544/1‑69 (MQ=255)
cTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAgc > 1:1389896/1‑69 (MQ=255)
cTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAg > 1:2502503/1‑68 (MQ=255)
cTGGGTAAAACCGGCGTTAACTTCGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAgc < 1:786047/69‑1 (MQ=255)
cTGGGTAAAACCGGCGTTAACTTCGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAgc < 1:3138120/69‑1 (MQ=255)
cTGGGTAAAACCGGCGTTAACTTCGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAgc < 1:1082862/69‑1 (MQ=255)
tGGGTAAAACCGGCGTTAACTTCGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAgc < 1:1411166/68‑1 (MQ=255)
aaaaCCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGAt > 1:1711929/1‑69 (MQ=255)
aaaaCCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGAt > 1:1976468/1‑69 (MQ=255)
tAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcg < 1:1573930/69‑1 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAgc > 1:2113963/1‑51 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:467835/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:944283/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:93903/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:2153543/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:2252162/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:2289564/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:3127318/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAAcgc > 1:2625508/1‑69 (MQ=255)
aaCTTCGGTGCGGGCATCACCGGCGGTTTCGCTTACGtt > 1:3176537/1‑39 (MQ=255)
cGGCGCGGGCATGACCTGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:175930/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:3424001/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:1262471/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:2457583/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:3188512/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:1903137/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:681821/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:1192096/1‑69 (MQ=255)
cGGCGCGGGCATGACCGGTGGCTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTaa > 1:241118/1‑69 (MQ=255)
|
AACGGTTGTGAATATATGACGGGTGGTATCGTCTGCATTCTGGGTAAAACCGGCGTTAACTTCGGTGCGGGCATGACCGGCGGTTTCGCTTACGTTCTCGATGAAAGCGGCGATTTCCGCAAACGCGTTAA > minE/2183910‑2184040
|
| 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
