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 |
|
A1 F3 I0 R2
|
260 |
44.3 |
3360226 |
90.5% |
3041004 |
64.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
3,815,914 |
T→C |
37.5% |
N702D (AAT→GAT) |
spoT ← |
bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,815,914 | 0 | T | C | 37.5%
| 51.7
/ 66.6
| 64 | N702D (AAT→GAT) | spoT | bifunctional (p)ppGpp synthetase II and guanosine‑3',5'‑bis pyrophosphate 3'‑pyrophosphohydrolase |
| Reads supporting (aligned to +/- strand): ref base T (25/15); new base C (9/15); total (34/30) |
| Fisher's exact test for biased strand distribution p-value = 7.15e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGC > W3110S.gb/3815855‑3815974
|
ccgccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATATAACATTAAtttcggtttcg < 1:2199927/69‑1 (MQ=255)
ccgccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtttcggtttcg < 1:2109456/69‑1 (MQ=255)
ccgccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtttcggtttcg < 1:1482468/69‑1 (MQ=255)
ccgccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtttcggtttcg < 1:2430371/69‑1 (MQ=255)
ccgccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtttcggtttcg < 1:981104/69‑1 (MQ=255)
ccgccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtttcggtttcg < 1:2369824/69‑1 (MQ=255)
ccgccTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGCTCATAAAACATTAAtttcggtttcg < 1:741278/69‑1 (MQ=255)
cTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtttcggtttcg < 1:3280957/65‑1 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAAtctcggttt > 1:1542198/1‑51 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTc > 1:450369/1‑71 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTc > 1:168919/1‑71 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTc > 1:1927472/1‑71 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTc > 1:1429454/1‑71 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTc > 1:2534155/1‑71 (MQ=255)
tCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGt > 1:254518/1‑70 (MQ=255)
gATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAAt < 1:416616/60‑1 (MQ=255)
gATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGAGTGACTTTAAt < 1:2993437/60‑1 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:222628/1‑71 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:578379/1‑71 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:604987/1‑71 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:1262217/1‑71 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:912725/1‑71 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:438410/1‑71 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:1704306/1‑71 (MQ=255)
gCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCa > 1:1865632/1‑71 (MQ=255)
cGTGTTGGGTTCATAAAACATTAATTTCGGTTTCTGGTGACTTTAATCACGTCTGGCATCACGCGGAtttt < 1:1633288/71‑1 (MQ=255)
cGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGAtttt < 1:422689/71‑1 (MQ=255)
ttGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTgcg < 1:2170808/70‑1 (MQ=255)
ttGGGTTCATAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTgcg < 1:3002507/70‑1 (MQ=255)
ggTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:1707586/71‑1 (MQ=255)
ggTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:688528/71‑1 (MQ=255)
ggTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:769782/71‑1 (MQ=255)
ggTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:2379783/71‑1 (MQ=255)
ggTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:3007841/71‑1 (MQ=255)
ggTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:55838/71‑1 (MQ=255)
ggTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:1982085/71‑1 (MQ=255)
gTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:906006/70‑1 (MQ=255)
gTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATg < 1:1794746/70‑1 (MQ=255)
tAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCAt < 1:2289291/64‑1 (MQ=255)
tAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCAt < 1:1146353/64‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:386319/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:3335315/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:518635/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:2216477/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:2714720/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:795337/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:1922768/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:1754571/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:1667988/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:1531300/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:989376/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:1237660/46‑1 (MQ=255)
tAAAACATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCAt < 1:999358/46‑1 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCATGCGGATTTTGCGCATGATATTCGc > 1:1126395/1‑68 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGc > 1:382325/1‑68 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGc > 1:1577442/1‑68 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGc > 1:803248/1‑68 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGc > 1:2470182/1‑68 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGc > 1:2497088/1‑68 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGc > 1:2640078/1‑68 (MQ=255)
cATTAATCTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGc > 1:642143/1‑68 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGTATTTTGCGCATGat > 1:3196887/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGAttt > 1:2249652/1‑48 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:252336/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:2852776/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:2483250/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:3017794/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:3025963/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:1688061/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:1677804/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:3058091/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:1519470/1‑58 (MQ=255)
aaTTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGat > 1:1067408/1‑58 (MQ=255)
|
CCGCCTGGCGAGCATTTCGCAGATGCGTGCATAACGTGTTGGGTTCATAAAACATTAATTTCGGTTTCGGGTGACTTTAATCACGTCTGGCATCACGCGGATTTTGCGCATGATATTCGC > W3110S.gb/3815855‑3815974
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
