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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
1,636,349 |
G→A |
26.0% |
A84V (GCG→GTG) |
tfaQ ← |
predicted tail fibre assembly protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 1,636,349 | 0 | G | A | 26.0%
| 92.1
/ 30.5
| 50 | A84V (GCG→GTG) | tfaQ | predicted tail fibre assembly protein |
| Reads supporting (aligned to +/- strand): ref base G (21/16); new base A (6/7); total (27/23) |
| Fisher's exact test for biased strand distribution p-value = 5.37e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
CCCTTCCGGCGATAACCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGATGACTCA > W3110S.gb/1636288‑1636417
|
cccTTCCGGCGATAACCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCg > 1:338899/1‑70 (MQ=35)
cccTTCCGGCGATAACCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCg > 1:4730701/1‑70 (MQ=35)
ccGGCGATAACCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGc > 1:3414778/1‑70 (MQ=35)
aaCCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACACGTCGCCGGAAGCCACGTCAt > 1:3424899/1‑70 (MQ=25)
aCCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATaa < 1:3489288/71‑1 (MQ=34)
aCCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATa > 1:10848/1‑70 (MQ=35)
aCCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATa < 1:1883089/70‑1 (MQ=35)
gTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCg < 1:1489223/70‑1 (MQ=35)
gTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCg < 1:3409785/70‑1 (MQ=35)
cATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCAc < 1:2229071/55‑1 (MQ=35)
cATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCAc < 1:2350244/55‑1 (MQ=35)
aTTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGttt < 1:893384/68‑1 (MQ=35)
tttCCGGTAACGGACCGAGTTCAGAAATAAATAACACGTCGCCGGAAGCCACGTCATAAACCGTTTTAccc > 1:641706/1‑71 (MQ=21)
ttCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTAcccc > 1:549692/1‑71 (MQ=34)
cGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCgat > 1:32282/1‑71 (MQ=34)
ggTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCgatg < 1:1360518/71‑1 (MQ=34)
gTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACAGttt > 1:4656954/1‑60 (MQ=255)
aCGGACCGAGTTCAGAAATAAATAACACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCg > 1:1237004/1‑64 (MQ=25)
aCGGACCGAGTTCAGAAATAAATAACACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCg > 1:1710076/1‑64 (MQ=25)
gACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTc > 1:707497/1‑70 (MQ=35)
gACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCa < 1:2029533/71‑1 (MQ=34)
ccGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCAt > 1:3306417/1‑43 (MQ=38)
ccGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCaa > 1:4034430/1‑70 (MQ=35)
cGAGTTCAGAAATAAATAACACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACg < 1:4781608/71‑1 (MQ=21)
cGAGTTCAGAAATAAATAACACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACg < 1:676429/71‑1 (MQ=21)
aGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGt > 1:3132905/1‑47 (MQ=38)
ttCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACgaga < 1:3121533/70‑1 (MQ=35)
cAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACgaga > 1:2894266/1‑68 (MQ=35)
cAGAAATAAATAACACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGc > 1:1330821/1‑71 (MQ=21)
aaataaatAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAAc < 1:3081682/61‑1 (MQ=35)
aataaataACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACg < 1:4083417/71‑1 (MQ=34)
aataaataACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACg < 1:4077769/71‑1 (MQ=34)
aataaataACACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCAc < 1:742562/70‑1 (MQ=25)
ataaataaCGCGTCGCCGGAAGCCACGTCATAAACCGtt > 1:3818111/1‑39 (MQ=40)
ataaataaCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTAc > 1:1927852/1‑43 (MQ=38)
taaataaCGCGTCGCCGGAAGCCACGTCATAAACCGttt < 1:4204702/39‑1 (MQ=40)
taaataaCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGAt < 1:3053049/71‑1 (MQ=34)
taaataaCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGAt < 1:2184124/71‑1 (MQ=34)
taaataaCACGTCGCCGGAAGCCACGTCATAAACCg < 1:4295302/36‑1 (MQ=255)
taaataaCACGTCGCCGGAAGCCACGTCATAAACCg < 1:3030656/36‑1 (MQ=255)
taaataaCACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGAt < 1:2172583/71‑1 (MQ=21)
aaataaCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGAt > 1:726858/1‑70 (MQ=35)
aataaCGCGTCGCCGGAAGCCCCGTCATAAACCGATTTACCCCGATGATCTTCAACGAGATGCCACGATgc > 1:1322366/1‑70 (MQ=255)
aataaCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTa > 1:2637281/1‑39 (MQ=40)
aataaCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTa > 1:3050140/1‑39 (MQ=40)
aataaCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCa > 1:3524719/1‑54 (MQ=35)
aataaCACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGATGa < 1:2632497/71‑1 (MQ=21)
aaCACGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGATGACt > 1:1335014/1‑70 (MQ=25)
aCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGATGACtca > 1:370910/1‑71 (MQ=34)
aCGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGATGACtca > 1:364845/1‑71 (MQ=34)
|
CCCTTCCGGCGATAACCAGGTAACATTTTCCGGTAACGGACCGAGTTCAGAAATAAATAACGCGTCGCCGGAAGCCACGTCATAAACCGTTTTACCCCGATGATCTTCAACGAGATGCCACGATGACTCA > W3110S.gb/1636288‑1636417
|
| 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
