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 |
|
A5 F21 I0 R2
|
316 |
65.6 |
5147759 |
97.4% |
5013917 |
60.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,678,206 |
C→T |
32.4% |
A1066T (GCT→ACT) |
yphG ← |
conserved hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,678,206 | 0 | C | T | 32.4%
| 69.1
/ 46.7
| 56 | A1066T (GCT→ACT) | yphG | conserved hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base C (20/16); new base T (10/8); total (31/25) |
| Fisher's exact test for biased strand distribution p-value = 1.00e+00 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.82e-01 |
TCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAG > W3110S.gb/2678149‑2678269
|
tCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCTAGCAGACTCa < 1:1570892/71‑1 (MQ=255)
aCGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCata > 1:3406095/1‑71 (MQ=255)
aCGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCata > 1:2573025/1‑71 (MQ=255)
cGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCatat < 1:3459901/71‑1 (MQ=255)
gtggtgAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGa > 1:398513/1‑57 (MQ=255)
gtgAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTgcgc < 1:806907/71‑1 (MQ=255)
tgAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCa < 1:4589996/71‑1 (MQ=255)
tgAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCa < 1:493854/62‑1 (MQ=255)
tgAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCa < 1:1267391/71‑1 (MQ=255)
gAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGa > 1:3213971/1‑52 (MQ=255)
gAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGa > 1:2640090/1‑52 (MQ=255)
aataatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAAc > 1:3919059/1‑71 (MQ=255)
aataatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAAc > 1:4704320/1‑71 (MQ=255)
ataatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTAATATTGCGCAAcc > 1:2967704/1‑71 (MQ=255)
ataatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGAGCGAGCAGACTCa < 1:4195216/59‑1 (MQ=255)
taatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGa > 1:3376696/1‑54 (MQ=255)
taatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCa < 1:4619311/52‑1 (MQ=255)
taatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCa < 1:4594828/52‑1 (MQ=255)
taatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCa < 1:2088675/52‑1 (MQ=255)
taatGCCGCTTTCGG‑CAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGa > 1:3114381/1‑53 (MQ=255)
aatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAAc > 1:422012/1‑68 (MQ=255)
aatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAAc > 1:1150000/1‑68 (MQ=255)
aatGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAAc > 1:4531765/1‑68 (MQ=255)
atGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTgcgc < 1:701583/64‑1 (MQ=255)
ccGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTcccc > 1:2598367/1‑70 (MQ=255)
ccGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCg < 1:4342323/71‑1 (MQ=255)
ccGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCg < 1:178361/71‑1 (MQ=255)
ccGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCg < 1:4872786/71‑1 (MQ=255)
tttCGGCCAAGCCGGATTAATCGCCGTCAATTCAGcgcg > 1:1767870/1‑39 (MQ=255)
tttCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTc > 1:2957438/1‑71 (MQ=255)
tttCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGAATCa < 1:4500042/49‑1 (MQ=255)
tttCGGCCAAGCCGGATTAATCGCCGTCAATTCAGAGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTc > 1:1819569/1‑71 (MQ=255)
tCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc > 1:666270/1‑71 (MQ=255)
gCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgcg > 1:3685318/1‑71 (MQ=255)
gCCAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCcgcg < 1:4150872/71‑1 (MQ=255)
cAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTc < 1:1367714/41‑1 (MQ=255)
cAAGCCGGATTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGa > 1:1314911/1‑71 (MQ=255)
cGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGc > 1:3403774/1‑69 (MQ=255)
ggATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAg < 1:1272588/71‑1 (MQ=255)
aTTAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa < 1:2453185/71‑1 (MQ=255)
ttAATCGCCGTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCAt > 1:3114124/1‑71 (MQ=255)
aaTCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa > 1:970112/1‑68 (MQ=255)
aaTCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCa > 1:3471937/1‑68 (MQ=255)
aaTCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGCCCCGCGGACGCCAGCATc < 1:3404222/70‑1 (MQ=255)
gCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGccac > 1:46800/1‑71 (MQ=255)
gTCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGAGGACGCCAGCATCGCCACCAt > 1:182928/1‑71 (MQ=255)
tCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc < 1:3576280/47‑1 (MQ=255)
tCAATTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTccc < 1:4309522/47‑1 (MQ=255)
tCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGc < 1:4057288/59‑1 (MQ=255)
tCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGc < 1:4896809/59‑1 (MQ=255)
tCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCAt > 1:1885731/1‑70 (MQ=255)
cAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGt < 1:3802756/43‑1 (MQ=255)
aaTTCAGTGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAg > 1:3817303/1‑71 (MQ=255)
aaTTCAGCGCGATCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAg > 1:5120031/1‑71 (MQ=255)
aaTTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGCCGCCAGCATCGCCACCATCAg > 1:3318534/1‑71 (MQ=255)
cAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGa > 1:2898457/1‑36 (MQ=255)
aGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCAt > 1:3208097/1‑54 (MQ=255)
|
TCACGGTGGTGAATAATGCCGCTTTCGGCCAAGCCGGATTAATCGCCGTCAATTCAGCGCGAGCAGACTCATATTGCGCAACCTCCCCGAGTCCCGCGGACGCCAGCATCGCCACCATCAG > W3110S.gb/2678149‑2678269
|
| 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
