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 F1 I0 R1
|
2892 |
75.3 |
5698161 |
66.1% |
3766484 |
59.5 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,259,793 |
C→T |
27.4% |
Q377Q (CAG→CAA) |
torZ ← |
trimethylamine N‑oxide reductase system III, catalytic subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,259,793 | 0 | C | T | 27.4%
| 75.4
/ 29.9
| 51 | Q377Q (CAG→CAA) | torZ | trimethylamine N‑oxide reductase system III, catalytic subunit |
| Reads supporting (aligned to +/- strand): ref base C (17/20); new base T (10/4); total (27/24) |
| Fisher's exact test for biased strand distribution p-value = 1.27e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01 |
CAACACGCGTCGGGTTGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTC > minE/1259723‑1259863
|
cAACACGCGTCGGGTTGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATc > 1:2102408/1‑71 (MQ=255)
aaCACGCGTCGGGTTGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCt > 1:109426/1‑71 (MQ=255)
cgTCGGGTTGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCt < 1:1088197/70‑1 (MQ=255)
cgTCGGGTTGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTa < 1:1946550/71‑1 (MQ=255)
tggggTTACCACCATTGGCAAAATGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCaa > 1:3184431/3‑70 (MQ=255)
tCGGGTTGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTa < 1:742430/69‑1 (MQ=255)
gTTACCACCATTGGCAAAATGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACAttg > 1:1004409/1‑69 (MQ=255)
ttaccaccaTTGGCAAAATGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATtgc > 1:2755281/4‑71 (MQ=255)
ttGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATcgc > 1:4433378/1‑71 (MQ=255)
taccaccaTTGGCAAAATGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATtgc > 1:239651/3‑70 (MQ=255)
gAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCAc < 1:3032831/71‑1 (MQ=255)
gAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCAc < 1:2844667/71‑1 (MQ=255)
aGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCAc > 1:4600250/1‑70 (MQ=255)
aaaTGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGc < 1:3618007/62‑1 (MQ=255)
aaaTGGTAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGAcga < 1:419678/69‑3 (MQ=255)
gtAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATcc < 1:4525914/70‑1 (MQ=255)
gtAAGAAAGACCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATcc < 1:138006/70‑1 (MQ=255)
tAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATc > 1:3898621/1‑69 (MQ=255)
gagaAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGc < 1:1149535/63‑1 (MQ=255)
gagaAACCAAAACCGCCGCACGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGc < 1:248870/63‑1 (MQ=255)
gaAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACAt > 1:3003638/1‑42 (MQ=255)
gaAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGtt > 1:2201941/1‑71 (MQ=255)
agaCCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCa > 1:402649/3‑65 (MQ=255)
gaCCAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGtttt > 1:4128930/2‑70 (MQ=255)
aaCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGc < 1:3615561/50‑1 (MQ=255)
aaCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCa < 1:908069/60‑1 (MQ=255)
aaCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTc < 1:2122035/71‑1 (MQ=255)
aCCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTc > 1:2733240/1‑70 (MQ=255)
ccAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCa > 1:2902326/1‑55 (MQ=255)
cAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATtgct > 1:3988192/1‑40 (MQ=12)
cAAAACCGCCGCCGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGtttt > 1:3137196/1‑67 (MQ=255)
cAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATcc < 1:1660741/60‑1 (MQ=255)
cAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgt < 1:3178490/63‑1 (MQ=255)
aaCCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCa > 1:5384322/1‑71 (MQ=255)
aaCCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCa > 1:2015270/1‑71 (MQ=255)
cgccgcCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGt < 1:317868/65‑1 (MQ=255)
gccgccGGGTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCACCa > 1:2928180/1‑70 (MQ=255)
gccgccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCa > 1:3376499/1‑70 (MQ=255)
cgccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTg < 1:5535675/61‑1 (MQ=255)
gccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGttt < 1:2246028/57‑1 (MQ=255)
gccCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATAtt < 1:4789950/71‑1 (MQ=255)
ccgggTGTGCCGATTTGCCCCAACATTGCTGCCAGCGTGACGATCATCCAGTGTTTTTGCTCa > 1:3004314/4‑63 (MQ=255)
cccGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTg > 1:2805669/1‑71 (MQ=255)
cGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGGATCCAGTGTTTCTGTTCACCATATTGCt < 1:3908737/71‑1 (MQ=255)
cGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAg > 1:1119392/1‑49 (MQ=255)
tgtACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGgc > 1:2667483/1‑71 (MQ=255)
tACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTg < 1:1224449/52‑1 (MQ=255)
tACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTg < 1:3432571/52‑1 (MQ=255)
ccAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgtgt > 1:1547495/1‑45 (MQ=255)
ccAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgtgt > 1:2318236/1‑45 (MQ=255)
ccAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAgtgt > 1:2839865/1‑45 (MQ=255)
tCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCt < 1:148507/60‑1 (MQ=255)
cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc > 1:4127653/1‑71 (MQ=255)
cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc > 1:3686733/1‑71 (MQ=255)
cTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTc > 1:761480/1‑71 (MQ=255)
|
CAACACGCGTCGGGTTGCCACCGTTGGAGTAATGATAAGAGAAACCAAAACCGCCGCCCGGTGTACCAATCTGCCCTAACATCGCCGCCAGCGTCACCAGCATCCAGTGTTTCTGTTCACCATATTGCTGGCGCTGAATTC > minE/1259723‑1259863
|
| 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
