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 |
4,328,660 |
C→T |
29.5% |
V125I (GTC→ATC) |
phnD ← |
phosphonate/organophosphate ester transporter subunit |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 4,328,660 | 0 | C | T | 29.5%
| 66.3
/ 32.5
| 44 | V125I (GTC→ATC) | phnD | phosphonate/organophosphate ester transporter subunit |
| Reads supporting (aligned to +/- strand): ref base C (17/14); new base T (4/9); total (21/23) |
| Fisher's exact test for biased strand distribution p-value = 1.94e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.93e-01 |
GCCAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTG > W3110S.gb/4328592‑4328727
|
gCCAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTtgatga > 1:3260146/1‑71 (MQ=255)
gCCAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTtgatga > 1:1462736/1‑71 (MQ=255)
ccAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTATTTGTTgatgat > 1:4318030/1‑71 (MQ=255)
aaaGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCa < 1:2803797/71‑1 (MQ=255)
aaaGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCa < 1:2382478/71‑1 (MQ=255)
ggTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAaca < 1:805213/71‑1 (MQ=255)
agaTCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCt > 1:2204488/1‑71 (MQ=255)
gaTCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTc > 1:3175648/1‑71 (MQ=255)
tCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTc > 1:1488356/1‑69 (MQ=255)
cTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTc > 1:3721082/1‑68 (MQ=255)
cTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAg > 1:4511205/1‑71 (MQ=255)
tttCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAg > 1:605254/1‑70 (MQ=255)
tCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGt < 1:903949/69‑1 (MQ=255)
ccGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTaa < 1:4793348/70‑1 (MQ=255)
agcagATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCa < 1:2177592/46‑1 (MQ=255)
aTCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATc < 1:2440887/40‑1 (MQ=255)
aTCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTc < 1:871542/49‑1 (MQ=255)
aTCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGt < 1:680036/53‑1 (MQ=255)
gcGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCa < 1:2216703/39‑1 (MQ=255)
cGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGa > 1:3489456/1‑36 (MQ=255)
cGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGa > 1:5030963/1‑36 (MQ=255)
cGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGa > 1:91929/1‑36 (MQ=255)
agTTCAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTAAc > 1:1886357/2‑54 (MQ=255)
ttCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCcgccgc < 1:2503075/71‑1 (MQ=255)
cAGGTTGTTGATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCTATCCATCCGCCGCGa > 1:1144634/1‑71 (MQ=255)
aGGTTGTTGATCGGACTGGCTTTGGTGACGAGCAACACGCTCCAGTAACGCGGCGATCCATCCGCcgcg < 1:1171654/69‑1 (MQ=255)
tgttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCgg > 1:4558540/1‑49 (MQ=255)
tgttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatcca > 1:4032144/1‑56 (MQ=255)
tgttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatcca > 1:5068451/1‑56 (MQ=255)
ttgATCGGACTGTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTc < 1:3297434/69‑1 (MQ=255)
ttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGat < 1:380168/51‑1 (MQ=255)
ttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGat < 1:5130291/51‑1 (MQ=255)
ttgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGat < 1:4342134/51‑1 (MQ=255)
tgATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatcc < 1:3667251/52‑1 (MQ=255)
aTCTGACTGTCTTTGTTGACGATCAACACGCTCCAGTAAc > 1:1445481/1‑40 (MQ=255)
aTCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatccat > 1:4494711/1‑52 (MQ=255)
aTCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatccat > 1:1295281/1‑52 (MQ=255)
aTCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGatccat > 1:3275923/1‑52 (MQ=255)
tCGGTCTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCg < 1:1975107/71‑1 (MQ=255)
tCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCg < 1:2033235/71‑1 (MQ=255)
aCTGTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAg < 1:3872786/70‑1 (MQ=255)
gTCTTTGTTGATGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGAcc < 1:3114789/55‑1 (MQ=255)
tCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTg > 1:74522/1‑71 (MQ=255)
tttGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATccgc < 1:1522796/45‑1 (MQ=255)
tttGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGAc > 1:1894236/1‑66 (MQ=255)
tgttgACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGcc < 1:4308366/70‑1 (MQ=255)
tgACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTg > 1:4490562/1‑71 (MQ=255)
|
GCCAAAGGTGAGATCTTTCCGCTTCGCCAGCAGATCGTTCAGGTTGTTGATCGGACTGTCTTTGTTGACGATCAACACGCTCCAGTAACCCGGCGATCCATCCGCCGCGACCGTCTGGGCGAAGACCTGGCCATTG > W3110S.gb/4328592‑4328727
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
