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 |
|
A54 F1 I1 R1
|
16 |
53.7 |
3449390 |
96.4% |
3325211 |
75.9 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
annotation |
gene |
description |
| RA |
REL606 |
2,897,276 |
C→T |
Q21* (CAA→TAA) |
yqeA → |
predicted amino acid kinase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | REL606 | 2,897,276 | 0 | C | T | 96.7%
| 213.1
/ NA
| 62 | Q21* (CAA→TAA) | yqeA | predicted amino acid kinase |
| Reads supporting (aligned to +/- strand): ref base C (2/0); new base T (38/21); total (41/21) |
| Fisher's exact test for biased strand distribution p-value = 5.41e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.99e-01 |
TGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGT > REL606/2897203‑2897346
|
tgagtgagGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTaa < 2:1286035/76‑1 (MQ=255)
tgagtgagGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTaa > 1:999984/1‑76 (MQ=255)
gtgagGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATg < 1:1559528/76‑1 (MQ=255)
tgagGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGa > 1:1035851/1‑76 (MQ=255)
gagGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGaa < 2:380777/76‑1 (MQ=255)
gagGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGaa > 1:68260/1‑76 (MQ=255)
agGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGaaa < 2:561163/76‑1 (MQ=255)
aaaaaTAAAAAAAAAAATTCTGCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCg < 1:1218855/76‑1 (MQ=255)
aaaTGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGt < 2:323292/76‑1 (MQ=255)
aaaTGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGt > 2:1201159/1‑76 (MQ=255)
aaTGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTa > 2:944835/1‑76 (MQ=255)
aTGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTaa > 2:330010/1‑76 (MQ=255)
tGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTaaa < 2:375619/76‑1 (MQ=255)
tGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTaaa < 2:1499671/76‑1 (MQ=255)
tGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTaaa < 1:336660/76‑1 (MQ=255)
tGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTaaa > 2:637826/1‑76 (MQ=255)
tGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGGaaa > 2:693983/1‑76 (MQ=255)
gAGTAAGAAAGTTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTaaaa < 1:1272328/76‑1 (MQ=255)
aGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTaaaaa < 2:729083/76‑1 (MQ=255)
gTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAAt > 2:119585/1‑76 (MQ=255)
aaGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTa > 2:268689/1‑76 (MQ=255)
aaaTTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTtc > 2:1702181/1‑76 (MQ=255)
ttGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCa > 2:635295/1‑76 (MQ=255)
ttGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCa > 2:1441864/1‑76 (MQ=255)
tGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAg > 2:892582/1‑76 (MQ=255)
gTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAgg > 1:1694754/1‑76 (MQ=255)
gTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAgg > 1:1448728/1‑76 (MQ=255)
ttCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGc > 1:1246570/1‑76 (MQ=255)
tctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCa > 2:1436733/1‑76 (MQ=255)
tctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCa > 1:723018/1‑76 (MQ=255)
ctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCaa > 2:166562/1‑76 (MQ=255)
ctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCaa > 2:715723/1‑76 (MQ=255)
ctcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGGAAATGGAAGCGGTAAAAATTACTTCTCAGGCaa > 2:283092/1‑76 (MQ=255)
tcGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAAt > 2:1235611/1‑76 (MQ=255)
cGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAAtt > 2:1141707/1‑76 (MQ=255)
ccTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAAttgtt > 2:1323388/1‑76 (MQ=255)
tGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGa < 1:56590/76‑1 (MQ=255)
gCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGAttt > 1:822996/1‑76 (MQ=255)
gCGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGAttt > 1:768110/1‑76 (MQ=255)
cGGGACTGCGCTGGGCGCTGACCTGGCCGGGTAAATGAAAGGGGTAAAACTTACTTCTCCGGAAATTGTTGATTTa > 2:129406/1‑76 (MQ=255)
cGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTa < 2:454637/76‑1 (MQ=255)
cGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTa > 2:129397/1‑76 (MQ=255)
cGGGAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTa < 2:663765/76‑1 (MQ=255)
gggAATGCGCTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTaa < 2:534044/76‑1 (MQ=255)
gcTGGGCGATGACCTGGCCGGGTAAATGACAGCGGTAAAAATTACTTCTAAGGCACTTGTTGATTCAATTGCCAAg > 2:583645/1‑76 (MQ=255)
gcTGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCCCAGGCAATTGTTGATTTAATTGCCCAg > 2:664623/1‑76 (MQ=255)
tGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAggg < 2:295188/76‑1 (MQ=255)
tGGGCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAggg > 2:1281729/1‑76 (MQ=255)
gggCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa > 1:767405/1‑76 (MQ=255)
gggCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa > 1:834379/1‑76 (MQ=255)
gggCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGa > 2:2682/1‑76 (MQ=255)
gCGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACa < 2:957042/76‑1 (MQ=255)
cGATGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACAt > 2:1316887/1‑76 (MQ=255)
aTGACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGa > 2:889416/1‑76 (MQ=255)
gACCTGGCCGGGTAAATGAAAGCGGTACAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAg > 2:634527/1‑76 (MQ=255)
gACCTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAg > 2:204904/1‑76 (MQ=255)
cTGGCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTa < 2:1448727/76‑1 (MQ=255)
ggCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTTCCCAGGGACATGAAGTTATc < 2:1363149/76‑1 (MQ=255)
ggCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATc > 1:1545729/1‑76 (MQ=255)
gCCGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCg < 2:370821/76‑1 (MQ=255)
ccGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGt > 1:727864/1‑76 (MQ=255)
ccGGGTAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGt < 2:1135395/76‑1 (MQ=255)
|
TGAGTGAGGAAAAATGAGTAAGAAAATTGTTCTCGCCCTGGGCGGGAATGCGCTGGGCGATGACCTGGCCGGGCAAATGAAAGCGGTAAAAATTACTTCTCAGGCAATTGTTGATTTAATTGCCCAGGGACATGAAGTTATCGT > REL606/2897203‑2897346
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 29 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
