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 |
|
A1 F3 I0 R1
|
560 |
56.4 |
4650532 |
94.9% |
4413354 |
59.3 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
642,134 |
A→G |
25.4% |
E275G (GAA→GGA) |
ybdR → |
predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 642,134 | 0 | A | G | 25.4%
| 92.8
/ 34.6
| 55 | E275G (GAA→GGA) | ybdR | predicted oxidoreductase, Zn‑dependent and NAD(P)‑binding |
| Reads supporting (aligned to +/- strand): ref base A (19/22); new base G (6/8); total (25/30) |
| 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 |
GGCAGGTCACCGGGGCGTGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAGTGTATTGCGGCGG > W3110S.gb/642066‑642202
|
ggCAGGTCACCGGGGCGTGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGaaa < 1:3420465/71‑1 (MQ=255)
gCAGGTCACCGGGGCGTGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAAc < 1:2406411/71‑1 (MQ=255)
aCCGGGGCGTGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCt > 1:4608432/1‑70 (MQ=255)
ggggCGTGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGAc > 1:1475637/1‑70 (MQ=255)
cGTGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTa < 1:3154916/68‑1 (MQ=255)
tGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGGAACgg < 1:227104/57‑1 (MQ=255)
tGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTaa < 1:806993/67‑1 (MQ=255)
tGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTa < 1:2897586/66‑1 (MQ=255)
gATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGGAACGGTg > 1:3799138/1‑57 (MQ=255)
gATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGGAACGGTg > 1:3568430/1‑57 (MQ=255)
gATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGa > 1:1953922/1‑70 (MQ=255)
gTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGa < 1:3656397/64‑1 (MQ=255)
tAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAAc < 1:485192/46‑1 (MQ=255)
tAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAAc < 1:2430743/46‑1 (MQ=255)
tAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAAc < 1:2377453/46‑1 (MQ=255)
tAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACg < 1:2048427/47‑1 (MQ=255)
aaTAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTg > 1:1954647/1‑49 (MQ=255)
aTAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCt > 1:3267482/1‑50 (MQ=255)
tAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGgc < 1:3558765/71‑1 (MQ=255)
gACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGaa < 1:492598/39‑1 (MQ=255)
gACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGa > 1:3292509/1‑49 (MQ=255)
gACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGgca < 1:1761161/70‑1 (MQ=255)
aCGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGGAACGGTGCTGACTAACCTGaa < 1:728328/58‑1 (MQ=255)
aCGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGGAACGGTGCTGACTAACCTGaa < 1:774926/58‑1 (MQ=255)
aCGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGGAACGGTGCTGACTAACCTGaa < 1:3397807/58‑1 (MQ=255)
aCGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGgcag > 1:1809718/1‑70 (MQ=255)
ccGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCagcagc < 1:3711100/71‑1 (MQ=255)
gTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTg < 1:1233478/39‑1 (MQ=255)
ggTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGa > 1:2847389/1‑56 (MQ=255)
ggTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTa > 1:3135718/1‑70 (MQ=255)
ttttGAAGCGAAAGGCAGCACCACGGGAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAg < 1:3090476/71‑1 (MQ=255)
ttttGAAGCGAAAGGCAGCACCACGGGAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCCGTAAAg < 1:3162752/71‑1 (MQ=255)
ttGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCg > 1:45403/1‑71 (MQ=255)
aaGGCAGCACCACGGGAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAg > 1:2057290/1‑71 (MQ=255)
aaGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCa < 1:3370821/70‑1 (MQ=255)
aaGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAg < 1:2166364/71‑1 (MQ=255)
gcagcaCCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAgtg < 1:1693189/70‑1 (MQ=255)
gcagcaCCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAgtg > 1:4218331/1‑70 (MQ=255)
agcaCCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAGTGTAt < 1:2976459/71‑1 (MQ=255)
gcaCCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGc < 1:3584177/55‑1 (MQ=255)
caccacGGGAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCg < 1:4195342/60‑1 (MQ=255)
accacGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGt > 1:193254/1‑55 (MQ=255)
ccacGGGAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAGTGTATTgcg > 1:1222005/1‑71 (MQ=255)
cacGGGAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAgtg < 1:2177522/63‑1 (MQ=255)
acGGGAACGGTGCTGACTAACCTGAAACTGGAGGgca > 1:3754647/1‑37 (MQ=255)
acGGGAACGGTGCTGACTAACCTGAAACTGGAGGgca > 1:2315515/1‑37 (MQ=255)
acGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGt > 1:4243834/1‑52 (MQ=255)
acGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGt > 1:2707866/1‑52 (MQ=255)
acGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGt > 1:3208006/1‑52 (MQ=255)
acGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGt > 1:509271/1‑52 (MQ=255)
cGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGt > 1:2382709/1‑51 (MQ=255)
cGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGt > 1:3055588/1‑51 (MQ=255)
cGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAGTGTATTgcggcg > 1:2722032/1‑71 (MQ=255)
ggAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAGTGTATTGcggcgg < 1:2308609/71‑1 (MQ=255)
ggAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAGTGTATTGcggcgg < 1:1714572/71‑1 (MQ=255)
gAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGt < 1:1422370/42‑1 (MQ=255)
gAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGt < 1:1290756/42‑1 (MQ=255)
|
GGCAGGTCACCGGGGCGTGGATGCAGTAATAGACGCCGTCGGTTTTGAAGCGAAAGGCAGCACCACGGAAACGGTGCTGACTAACCTGAAACTGGAGGGCAGCAGCGGTAAAGCGTTGCGTCAGTGTATTGCGGCGG > W3110S.gb/642066‑642202
|
| 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
