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 |
3,259,237 |
G→A |
32.0% |
S613F (TCT→TTT) |
tdcE ← |
pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 3,259,237 | 0 | G | A | 32.0%
| 63.8
/ 42.3
| 50 | S613F (TCT→TTT) | tdcE | pyruvate formate‑lyase 4/2‑ketobutyrate formate‑lyase |
| Reads supporting (aligned to +/- strand): ref base G (22/12); new base A (6/10); total (28/22) |
| Fisher's exact test for biased strand distribution p-value = 1.26e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01 |
CGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTAATTTTCTTCAT > W3110S.gb/3259167‑3259307
|
cGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAg < 1:794719/71‑1 (MQ=255)
gcgAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGaa > 1:4813629/1‑69 (MQ=255)
gcgAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAAAAGt < 1:4757252/71‑1 (MQ=255)
gcgAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAAAAGt < 1:319439/71‑1 (MQ=255)
aaCGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGa > 1:1215537/1‑70 (MQ=255)
aCGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGa > 1:3002819/1‑69 (MQ=255)
gcgcGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGa < 1:5091881/71‑1 (MQ=255)
gacgacCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTgg < 1:690173/71‑1 (MQ=255)
gacgacCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTgg > 1:2673970/1‑71 (MQ=255)
actacCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTggg > 1:4117847/4‑71 (MQ=255)
acgacCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTggg > 1:1690367/1‑71 (MQ=255)
cgacCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTggg > 1:1680746/1‑70 (MQ=255)
acCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGt < 1:11623/48‑1 (MQ=255)
ccGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGAc > 1:3258606/1‑63 (MQ=255)
cGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGa > 1:4175449/1‑48 (MQ=255)
ccGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACg > 1:4264632/1‑71 (MQ=255)
ccGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACg > 1:765459/1‑71 (MQ=255)
cGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACg > 1:341451/1‑70 (MQ=255)
gCGTATTACCGGTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTggg < 1:1870990/60‑1 (MQ=255)
tATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATc < 1:1212392/50‑1 (MQ=255)
tATTACCGGTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTg < 1:248087/55‑1 (MQ=255)
ttACCGGTTTTCTGGCCGTACACCACGTTAGAAGt < 1:2235857/35‑1 (MQ=255)
ttACCGGTTTTCTGGCCGTACACCACGTTAGAAGt < 1:4076890/35‑1 (MQ=255)
ttACCGGTTTTCTGGCCGTACACCACGTTAGAAGt < 1:1157360/35‑1 (MQ=255)
ttACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGc < 1:2685978/70‑1 (MQ=255)
ttACCGGTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGc < 1:1505049/70‑1 (MQ=255)
tACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTTCGa > 1:4591172/1‑71 (MQ=255)
tACCGGTTTTCTGGCCGTACACCACGTTAAAAGTg > 1:2748792/1‑35 (MQ=255)
tACCGGTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGa > 1:2500865/1‑49 (MQ=255)
aCCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGaa > 1:2993225/1‑44 (MQ=255)
aCCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGaa > 1:57217/1‑44 (MQ=255)
aCCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGa > 1:2442538/1‑48 (MQ=255)
aCCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGa > 1:2139440/1‑48 (MQ=255)
aCCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGa > 1:2162741/1‑48 (MQ=255)
aCCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGa > 1:1282828/1‑70 (MQ=255)
cGGTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCg > 1:1595207/1‑62 (MQ=255)
ggTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAgg > 1:3267638/1‑71 (MQ=255)
ggTTTTCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAgg > 1:582918/1‑71 (MQ=255)
gTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAg > 1:4949372/1‑38 (MQ=255)
tttCTGGCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTGGGTAGGGACGGc < 1:4645722/57‑1 (MQ=255)
gCCGTACACCACGTTAAAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAgcg < 1:2256720/71‑1 (MQ=255)
gTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTgg < 1:3889919/63‑1 (MQ=255)
caccacGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTa < 1:2185586/70‑1 (MQ=255)
caccacGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTa < 1:1754471/70‑1 (MQ=255)
caccacGTTAAAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAgcg < 1:551085/65‑1 (MQ=255)
ccacGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTAAtt < 1:6323/71‑1 (MQ=255)
cacGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATa > 1:848303/1‑51 (MQ=255)
cacGTTAAAAGTGATAGTCAGAATCGACTGGGTAgg < 1:3503242/36‑1 (MQ=255)
cGTTAAAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTa < 1:286877/65‑1 (MQ=255)
aGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTAATTTTCTTCa > 1:4836105/1‑71 (MQ=255)
aGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTAATTTTCTTCa > 1:2726629/1‑71 (MQ=255)
gAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTAATTTTCTTCAt < 1:676626/71‑1 (MQ=255)
gAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTAATTTTCTTCAt < 1:3182343/71‑1 (MQ=255)
|
CGGCGCGAACGGTGTTCCGGCGCGACGACCGTCCGGCGTATTACCGGTTTTCTGGCCGTACACCACGTTAGAAGTGATAGTCAGAATCGACTGGGTAGGGACGGCGTTGCGATAGGTTGGCAGCGCTTTAATTTTCTTCAT > W3110S.gb/3259167‑3259307
|
| 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
