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 |
2,967,832 |
T→C |
63.5% |
T220T (ACT→ACC) |
deoD → |
purine‑nucleoside phosphorylase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 2,967,832 | 0 | T | C | 63.5%
| 44.4
/ 40.9
| 71 | T220T (ACT→ACC) | deoD | purine‑nucleoside phosphorylase |
| Reads supporting (aligned to +/- strand): ref base T (22/4); new base C (40/5); total (62/9) |
| Fisher's exact test for biased strand distribution p-value = 7.16e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.48e-05 |
CCGTATCTGACCACATCCGCACTCACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTGGGCGATAAAGAGTAATTGT > minE/2967777‑2967896
|
ccGTATCTGACCACATCCGCACTCACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGAc < 1:2100609/68‑1 (MQ=255)
ccGTATCTGACCACATCCGCACTCACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGAc < 1:2704443/68‑1 (MQ=255)
ccGTATCTGACCACATCCGCACTCACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGAc < 1:3319647/68‑1 (MQ=255)
cacaTCCGCACTCACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCAAAAt > 1:2550891/1‑68 (MQ=255)
cGCACTCACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCAAAATCGCACt > 1:2727706/1‑68 (MQ=255)
cACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCaa > 1:3259940/1‑53 (MQ=255)
cACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCaa > 1:3263591/1‑53 (MQ=255)
cACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCaa > 1:789723/1‑53 (MQ=255)
aCGAGCGGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATcc > 1:258748/1‑68 (MQ=255)
aCGAGCGGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:8375/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGCCCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:395787/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCaaa > 1:54034/1‑53 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATcc > 1:259160/1‑68 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATcc > 1:435286/1‑68 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATcc > 1:649846/1‑68 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATcc > 1:715787/1‑68 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATcc > 1:1055050/1‑68 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:104357/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:3282230/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:2716295/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:47459/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:3208956/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:722508/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:1790832/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:807089/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:1232462/1‑69 (MQ=255)
aCGAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg > 1:9717/1‑69 (MQ=255)
gAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg < 1:2096581/67‑1 (MQ=255)
gAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg < 1:2258944/67‑1 (MQ=255)
gAGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg < 1:2513491/67‑1 (MQ=255)
gAGCAGACCACTGACGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg < 1:1378510/67‑1 (MQ=255)
aGCAGACCACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCg < 1:815356/66‑1 (MQ=255)
cAGACCACTGCCGCTGAACGTCAGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTctg > 1:2919040/1‑69 (MQ=255)
cAGACCACTGCCGCTGAACGTCAGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTctg > 1:2444687/1‑69 (MQ=255)
cAGACCACTGCCGCTGAACGTCAGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTctg > 1:1401470/1‑69 (MQ=255)
ccACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg < 1:1977738/69‑1 (MQ=255)
cACTGCCGCTGAGCGTCAGACCTCCTTCAACGACATGATCAAAATCCCACTGGAATCCGTTCTGCTgg > 1:2294294/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCg > 1:3074480/1‑47 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGt > 1:3156154/1‑60 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:874346/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:1028257/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:994526/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:630296/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:3112945/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:491168/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:3072537/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:1880198/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:1895729/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:1779100/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:1439322/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:1409408/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:231713/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:1189676/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:2610746/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:2870545/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:2874527/1‑68 (MQ=255)
cACTGCCGCTGAGCGTCAGACCACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTgg > 1:2944464/1‑68 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:905875/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:1075598/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:1066558/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:1505624/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:3150040/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:1876452/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:2015585/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:20892/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:21828/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:409682/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:2483809/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTc > 1:2655353/1‑45 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTGGGCGATAAAGAGTAATtgt > 1:2026940/1‑69 (MQ=255)
aGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTGGGCGATAAAGAGTAATtgt > 1:2625217/1‑69 (MQ=255)
|
CCGTATCTGACCACATCCGCACTCACGAGCAGACCACTGCCGCTGAGCGTCAGACTACCTTCAACGACATGATCAAAATCGCACTGGAATCCGTTCTGCTGGGCGATAAAGAGTAATTGT > minE/2967777‑2967896
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
