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 |
2,791,709 |
G→A |
40.2% |
L110L (TTG→TTA) |
ubiC → |
chorismate pyruvate lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,791,709 | 0 | G | A | 40.2%
| 31.4
/ 49.0
| 72 | L110L (TTG→TTA) | ubiC | chorismate pyruvate lyase |
| Reads supporting (aligned to +/- strand): ref base G (5/38); new base A (8/21); total (13/59) |
| Fisher's exact test for biased strand distribution p-value = 1.19e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
GCTTGCCGGTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAT > minE/2791643‑2791774
|
gCTTGCCGGTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTgg > 1:2530782/1‑68 (MQ=255)
gCTTGCCGGTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTgg > 1:748661/1‑68 (MQ=255)
gCTTGCCGGTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTgg > 1:743566/1‑68 (MQ=255)
gCTTGCCGGTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTg > 1:1210602/1‑67 (MQ=255)
tGCCGGTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTaa < 1:839510/69‑1 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGt > 1:1032780/1‑62 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGt > 1:3364245/1‑62 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGt > 1:2088731/1‑62 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGt > 1:2073543/1‑62 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGt > 1:1851536/1‑62 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGt > 1:1734473/1‑62 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGt > 1:1552584/1‑62 (MQ=255)
gTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTAGCGTTACAAAAATTAGGt > 1:1360361/1‑62 (MQ=255)
cgtcgtTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAgg > 1:2907967/1‑69 (MQ=255)
cgtcgtTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAg > 1:1651599/1‑68 (MQ=255)
gtTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGc < 1:3003232/69‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:1533092/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:3129499/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:3228171/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:2268479/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:3288728/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:2151708/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:2136725/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:97562/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:2030412/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:654472/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:1333965/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:1865459/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:1919706/68‑1 (MQ=255)
tCCTGTGTCAACGTTAAGCGGGCCGCAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:2264955/68‑1 (MQ=255)
ccTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:1317682/67‑1 (MQ=255)
ccTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:2488158/67‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:1982855/41‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:3251135/41‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:1305196/41‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:2092190/41‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:199309/41‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:987768/41‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:2698087/41‑1 (MQ=255)
aaCGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:1522125/41‑1 (MQ=255)
gTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCAcatc < 1:1754085/69‑1 (MQ=255)
gTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTAGGTa < 1:2320803/38‑1 (MQ=255)
cGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGa < 1:3286551/68‑1 (MQ=255)
cGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGa < 1:3305299/68‑1 (MQ=255)
cGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGa < 1:3034828/68‑1 (MQ=255)
cGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGa < 1:998066/68‑1 (MQ=255)
cGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGa < 1:1106183/68‑1 (MQ=255)
cGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGa < 1:2394041/68‑1 (MQ=255)
cGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGa < 1:2252739/68‑1 (MQ=255)
gCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTAACATCATCGa < 1:3215656/65‑1 (MQ=255)
cGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCATTAGGACGCTATCTGTTCACATCATCGACATTaa < 1:654113/69‑1 (MQ=255)
gCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAAccc > 1:422522/1‑68 (MQ=255)
tGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCggg < 1:139049/69‑1 (MQ=255)
tGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCggg < 1:1708971/69‑1 (MQ=255)
gCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCt < 1:3238001/37‑1 (MQ=255)
aCAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTa > 1:3391234/1‑68 (MQ=255)
aCAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTa > 1:2748882/1‑68 (MQ=255)
aaaaTTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTga < 1:2232857/69‑1 (MQ=255)
aaaaTTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTga < 1:417767/69‑1 (MQ=255)
aaaaTTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTga < 1:784951/69‑1 (MQ=255)
aaaaTTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTga < 1:648953/69‑1 (MQ=255)
aaaaTTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTga < 1:3016579/69‑1 (MQ=255)
aaaaTTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTga < 1:153252/69‑1 (MQ=255)
aaaaTTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTga < 1:2865740/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:2987168/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:2256200/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:1179749/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:1311470/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:2992280/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:714136/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:1805654/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:509896/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:293678/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:2129805/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:2135451/69‑1 (MQ=255)
aTTAGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAt < 1:2297144/69‑1 (MQ=255)
|
GCTTGCCGGTCGTACCGTCGTTCCTGTGTCAACGTTAAGCGGGCCGGAGCTGGCGTTACAAAAATTGGGTAAAACGCCGTTAGGACGCTATCTGTTCACATCATCGACATTAACCCGGGACTTTATTGAGAT > minE/2791643‑2791774
|
| 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
