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 |
2,627,716 |
T→C |
27.3% |
I62I (ATT→ATC) |
livJ → |
leucine/isoleucine/valine transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,627,716 | 0 | T | C | 27.3%
| 89.7
/ 33.8
| 84 | I62I (ATT→ATC) | livJ | leucine/isoleucine/valine transporter subunit |
| Reads supporting (aligned to +/- strand): ref base T (43/18); new base C (11/12); total (54/30) |
| Fisher's exact test for biased strand distribution p-value = 7.40e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.44e-01 |
AGTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGC > minE/2627649‑2627778
|
aGTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTa < 1:2478350/69‑1 (MQ=255)
aGTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTa < 1:303625/69‑1 (MQ=255)
gTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTaa > 1:2293922/1‑69 (MQ=255)
gTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTaa > 1:709507/1‑69 (MQ=255)
gTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTaa > 1:635529/1‑69 (MQ=255)
gTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTaa > 1:58305/1‑69 (MQ=255)
gTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTaa > 1:3395974/1‑69 (MQ=255)
gTACGGTGACCAGGAGGTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTaa > 1:2490717/1‑69 (MQ=255)
aCGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTaaa > 1:3393415/1‑68 (MQ=255)
cGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAg > 1:2466989/1‑68 (MQ=255)
cGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAg > 1:1500980/1‑68 (MQ=255)
cGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAg > 1:3205523/1‑68 (MQ=255)
cGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAg > 1:3058623/1‑68 (MQ=255)
gTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGc < 1:3127653/68‑1 (MQ=255)
aCCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGcaaca < 1:993730/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:3155579/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:674234/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:2855373/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:683802/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:938557/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:939094/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:2838061/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:2206665/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:2183156/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:1171060/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:1595870/69‑1 (MQ=255)
aGGAGTTTACTGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAAc < 1:186553/69‑1 (MQ=255)
gTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCa > 1:1440415/1‑69 (MQ=255)
gTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCa > 1:1509812/1‑69 (MQ=255)
gTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCa > 1:490858/1‑69 (MQ=255)
gTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCa > 1:2844070/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:1955485/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:2147211/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:1079488/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:842715/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:772133/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:67877/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:3278630/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:2861789/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:2777476/1‑69 (MQ=255)
tACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAAt > 1:2097566/1‑69 (MQ=255)
tACCGGAGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCAtt > 1:6098/1‑49 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAGGGCAACAAACTGCAAATCg > 1:2125563/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:3390428/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:2069736/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:667680/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:522364/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:2538341/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:2759442/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:1700805/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:2869925/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGCAACAAACTGCAAATCg > 1:1859017/2‑68 (MQ=255)
tggCGCAGAGCAGGCGGTTGCGGATATCAATGCTAAAGGTGGTATCAAAGGAAACAAACTGCAAATCg > 1:3372450/2‑68 (MQ=255)
cGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGTCGGCATTAAAGGcaact < 1:846767/56‑2 (MQ=255)
cAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGAc < 1:2545670/69‑1 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGTCGATGCCtgt > 1:362126/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCtgt > 1:1348027/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCtgt > 1:47390/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCtgt > 1:2080066/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCtgt > 1:1630321/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCtgt > 1:1046450/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCtgt > 1:311844/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCtgt > 1:3093772/1‑69 (MQ=255)
gCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTCCAAATCGTAAAATATGACGATGCCtgt > 1:1407478/1‑69 (MQ=255)
atCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGAccc > 1:2984028/1‑68 (MQ=255)
aaCGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGa > 1:3137931/1‑67 (MQ=255)
aaCGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGa > 1:1920010/1‑67 (MQ=255)
cTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAgg > 1:2562837/1‑69 (MQ=255)
cTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAgg > 1:2588866/1‑69 (MQ=255)
cTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAgg > 1:2425867/1‑69 (MQ=255)
cTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAgg > 1:155557/1‑69 (MQ=255)
cTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAgg > 1:2929862/1‑69 (MQ=255)
cTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAgg > 1:3048615/1‑69 (MQ=255)
gcggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGa < 1:2687608/57‑1 (MQ=255)
gcggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGa < 1:2041899/57‑1 (MQ=255)
gcggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGa < 1:169989/57‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATTCCTGTGACCCGAAACAGGCGGTTGc < 1:1328322/69‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:674206/69‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:2683963/69‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:1449484/69‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:2287639/69‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:3203513/69‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:847537/69‑1 (MQ=255)
cggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:1757572/69‑1 (MQ=255)
ggcATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGc < 1:3271665/68‑1 (MQ=255)
|
AGTACGGTGACCAGGAGTTTACCGGCGCAGAGCAGGCGGTTGCGGATATCAACGCTAAAGGCGGCATTAAAGGCAACAAACTGCAAATCGTAAAATATGACGATGCCTGTGACCCGAAACAGGCGGTTGC > minE/2627649‑2627778
|
| 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
