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 |
2,060,531 |
C→T |
53.3% |
A242A (GCG→GCA) |
ygjD ← |
predicted peptidase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,060,531 | 0 | C | T | 53.3%
| 0.2
/ 36.2
| 45 | A242A (GCG→GCA) | ygjD | predicted peptidase |
| Reads supporting (aligned to +/- strand): ref base C (5/16); new base T (22/2); total (27/18) |
| Fisher's exact test for biased strand distribution p-value = 3.44e-06 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.56e-01 |
GACCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGTCACGAAT > minE/2060465‑2060593
|
gACTAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGc < 1:729525/69‑1 (MQ=255)
gACCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGc < 1:2716416/69‑1 (MQ=255)
gACCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGc < 1:390540/69‑1 (MQ=255)
gACCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGc < 1:707861/69‑1 (MQ=255)
gACCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGc < 1:1936050/69‑1 (MQ=255)
gACCAGACGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGc < 1:1927587/69‑1 (MQ=255)
aCCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCa < 1:1370577/69‑1 (MQ=255)
aCCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCa < 1:3075305/69‑1 (MQ=255)
aCCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCa < 1:2296548/69‑1 (MQ=255)
aCCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCa < 1:1923632/69‑1 (MQ=255)
aCCAGTCGCTTAAAGCACGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCa < 1:946960/69‑1 (MQ=255)
cGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCATCTTCa < 1:472250/69‑1 (MQ=255)
cGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCATCTTCa < 1:142043/69‑1 (MQ=255)
cTGATCCAGTGCTCGCTTACACTTAATCATCAACGTATCGACCACTGCATCTTCAAAGGCGCGGGCGat < 1:3213220/69‑1 (MQ=255)
cTGATCCAGTGCTCGCTTACACTTAATCATCAACGTATCGACCACTGCATCTTCAAAGGCGCGGGCGat < 1:1456443/69‑1 (MQ=255)
aGCGTATCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGgtcg > 1:2410852/1‑57 (MQ=255)
aGCGTATCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGtt > 1:1295602/1‑68 (MQ=255)
cGTATCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGt < 1:838851/68‑1 (MQ=255)
cGTATCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGt < 1:1008451/68‑1 (MQ=255)
cGTATCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGt < 1:1073897/68‑1 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:850981/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:965080/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:823373/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:3384729/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:3181961/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:312724/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:2862133/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:2181912/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:1145663/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:1171232/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:1306273/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:1665230/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:1882785/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:2712283/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:2267723/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:2405909/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:2668/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACgt > 1:2674277/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACg > 1:369174/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACg > 1:3367249/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAGTGCCGTTGTCACg > 1:1300775/1‑68 (MQ=255)
tCGACCACTGCATCTTCAAAGGCGCGGGCGATATCGGCACGCGTCTGATCGTCAATGCCGTTGTCACgt > 1:2273577/1‑68 (MQ=255)
tCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGTCACGa > 1:2199171/1‑69 (MQ=255)
gACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGTCACGAAt > 1:2154597/1‑69 (MQ=255)
gACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGTCACGAAt > 1:1958417/1‑69 (MQ=255)
|
GACCAGTCGCTTAAAGCCCGTCTGATCCAGCGCCCGCTTGCACTTAATCATCAGCGTATCGACCACCGCATCTTCAAAGGCGCGGGCGATATCAGCACGCGTCTGGTCGTCGGTGCCGTTGTCACGAAT > minE/2060465‑2060593
|
| 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
