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 |
|
A6 F21 I0 R1
|
2169 |
63.0 |
3952800 |
76.2% |
3012033 |
62.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
965,844 |
A→T |
53.5% |
V17D (GTT→GAT) |
ydeM ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 965,844 | 0 | A | T | 53.5%
| 5.1
/ 59.7
| 43 | V17D (GTT→GAT) | ydeM | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base A (12/8); new base T (13/10); total (25/18) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.60e-01 |
TTTCAGAGTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTC > minE/965774‑965902
|
tttCAGAGTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTaaa > 1:1144079/1‑71 (MQ=255)
tttCAGAGTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTaaa > 1:429896/1‑71 (MQ=255)
gTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGAt > 1:1923878/1‑71 (MQ=255)
catcaatcCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTga > 1:1152027/1‑66 (MQ=255)
atccatccATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGAtt > 1:1129341/1‑69 (MQ=255)
tccatccaTTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACa < 1:3514408/71‑1 (MQ=255)
tccatccaTTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACa < 1:1858740/71‑1 (MQ=255)
catTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGaaa < 1:37416/71‑1 (MQ=255)
catTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGaaa < 1:3935911/71‑1 (MQ=255)
catTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGaa > 1:3104215/1‑70 (MQ=255)
atTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGaaaa > 1:1519516/1‑71 (MQ=255)
ttttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACt > 1:2559661/1‑71 (MQ=255)
ttttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTAc > 1:729604/1‑61 (MQ=255)
tttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTg > 1:1099517/1‑71 (MQ=255)
ttCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTg > 1:546801/1‑70 (MQ=255)
gAGTAAACTCCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTg < 1:1386468/65‑1 (MQ=255)
gTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCtt < 1:732623/71‑1 (MQ=255)
tAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAg < 1:2583518/65‑1 (MQ=255)
aaaCTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTgg > 1:999083/1‑71 (MQ=255)
aaCTGCGACTCTTTTTCAAGGTAAAAACAGTAAtcac > 1:1778015/1‑37 (MQ=255)
aaCTGCGACTCTTTTTCAAGGTAAAAACAGTAATCACAt > 1:2754660/1‑39 (MQ=255)
aaCTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGc > 1:2584222/1‑71 (MQ=255)
gCGACTCTTTTTCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGt > 1:2985114/1‑70 (MQ=255)
cGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGt < 1:3503556/69‑1 (MQ=255)
cGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGt < 1:106854/69‑1 (MQ=255)
gACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAAc > 1:1026943/1‑71 (MQ=255)
ctctTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACAt > 1:479193/1‑43 (MQ=255)
ctctTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGt > 1:2603957/1‑71 (MQ=255)
tctTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGaa < 1:2803329/46‑1 (MQ=255)
tctTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACg > 1:474004/1‑69 (MQ=255)
tttttCAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAAc < 1:3695520/47‑1 (MQ=255)
tttttCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAAc > 1:2784247/1‑66 (MQ=255)
tttttCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAAc > 1:2179576/1‑66 (MQ=255)
ttCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCg > 1:1444346/1‑71 (MQ=255)
cAAGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGc > 1:2017909/1‑70 (MQ=255)
aaGTTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCt < 1:453463/70‑1 (MQ=255)
aaGGTAAAAACAGTAATCACATTTGAGATTACATTGa < 1:3394254/37‑1 (MQ=255)
aaGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCt < 1:648278/70‑1 (MQ=255)
aaGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTa < 1:2706819/71‑1 (MQ=255)
aGGTAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAt < 1:293373/71‑1 (MQ=255)
tAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAtctc > 1:2406751/1‑71 (MQ=255)
tAAAAACAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGAATCGCTAtctc > 1:3282730/1‑71 (MQ=255)
aaaaCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAtct < 1:1545881/68‑1 (MQ=255)
aaaaCAGTAATCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTAt > 1:2285101/1‑66 (MQ=255)
aaaCAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGt > 1:2211110/1‑55 (MQ=255)
aGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTaa < 1:3119882/48‑1 (MQ=255)
aaaCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCg < 1:126756/54‑1 (MQ=255)
aaCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGt > 1:1970901/1‑47 (MQ=255)
aaCACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGt > 1:24235/1‑47 (MQ=255)
|
TTTCAGAGTGCTGTCATCCATCCATTTTTCATGAGTAAACTGCGACTCTTTTTCAAGGTAAAAACAGTAAACACATTTGAGATTACATTGAAAACTGGAGGGCTTGGCTGTAACGTGCATCGCTATCTC > minE/965774‑965902
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
