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 |
1,981,954 |
T→C |
40.0% |
T41A (ACG→GCG) |
yggR ← |
predicted transporter |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,981,954 | 0 | T | C | 40.0%
| 17.5
/ 33.1
| 50 | T41A (ACG→GCG) | yggR | predicted transporter |
| Reads supporting (aligned to +/- strand): ref base T (16/14); new base C (11/9); total (27/23) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00 |
CTCCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTG > minE/1981889‑1982012
|
ctcCAGCAATATTGCCCGCTTATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGATGTCCGGCGTAt > 1:376660/1‑68 (MQ=255)
ctcCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTa > 1:1618404/1‑67 (MQ=255)
ctcCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTAt > 1:2762941/1‑68 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:2655661/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:982912/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:77463/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:3082087/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:2889780/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:1046925/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:2389312/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:2168160/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:2056264/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:2050006/1‑69 (MQ=255)
aGCAATATTGTCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAAc > 1:1756509/1‑69 (MQ=255)
atTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCa > 1:906659/1‑69 (MQ=255)
atTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCa > 1:1375543/1‑69 (MQ=255)
ttGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGgcgc > 1:513583/1‑67 (MQ=255)
ttGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAg > 1:3155912/1‑69 (MQ=255)
ttGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAg > 1:1478514/1‑69 (MQ=255)
ttGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAg > 1:769989/1‑69 (MQ=255)
ttGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAg > 1:1941692/1‑69 (MQ=255)
cGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGc > 1:2486326/1‑69 (MQ=255)
cGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGc > 1:1263256/1‑69 (MQ=255)
cGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGc > 1:3076851/1‑69 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:163945/53‑1 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:531905/53‑1 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:871996/53‑1 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:1925096/53‑1 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:1094664/53‑1 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:3385991/53‑1 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:1155825/53‑1 (MQ=255)
gCCACTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:3103233/53‑1 (MQ=255)
aCTCCCGCAGTAGCTCTTCGACGTCCAGCGCATCAAACGGCGCAGCTTcc < 1:584654/50‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCTCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:1055592/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:3206256/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:1357118/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:503915/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:2694067/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:2226318/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:550059/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:2190508/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:1677458/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:899592/69‑1 (MQ=255)
tCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCAt < 1:181939/69‑1 (MQ=255)
cccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCcgcg < 1:2764873/58‑1 (MQ=255)
cccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATc > 1:2132210/1‑69 (MQ=255)
cccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATc > 1:1085488/1‑69 (MQ=255)
cccGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATc > 1:901536/1‑69 (MQ=255)
cGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTg < 1:373038/68‑1 (MQ=255)
cGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTg < 1:1848010/68‑1 (MQ=255)
|
CTCCAGCAATATTGCCCGCTGATCGTCATCCAGCCACTCCCGCAGTAGCTCTTCGACGTCCGGCGTATCAAACGGCGCAGCTTCCATTCTGCCGCGAATGCGCCATCGTGCGGGCCAGGCGCTG > minE/1981889‑1982012
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
