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 F21 I0 R2
|
308 |
27.9 |
1975068 |
96.7% |
1909890 |
67.2 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,893,179 |
A→C |
100% |
I110L (ATT→CTT) |
ygcP → |
predicted anti‑terminator regulatory protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | W3110S.gb | 2,893,179 | 0 | A | C | 92.9%
| 96.2
/ ‑2.3
| 28 | I110L (ATT→CTT) | ygcP | predicted anti‑terminator regulatory protein |
| Reads supporting (aligned to +/- strand): ref base A (2/0); new base C (19/7); total (21/7) |
| 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 |
| Rejected as polymorphism: E-value score below prediction cutoff. |
| Rejected as polymorphism: Variant not supported by required number of reads on each strand. |
ACCAAAGCCTCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGA > W3110S.gb/2893116‑2893237
|
aCCAAAGCCTCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGa > 1:356054/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTa > 1:1390162/1‑49 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTa > 1:1755111/1‑49 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTa > 1:142823/1‑49 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTa > 1:1431179/1‑49 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTa > 1:1448311/1‑49 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:653113/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:1894968/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:389433/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:422812/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:1640825/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:1410234/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:845591/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:1363869/1‑71 (MQ=255)
ttGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTca > 1:858176/1‑71 (MQ=255)
aaaGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCacaa < 1:582896/71‑1 (MQ=255)
aaaGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCacaa < 1:528708/71‑1 (MQ=255)
aaaGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCacaa < 1:470408/71‑1 (MQ=255)
aaaGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCacaa < 1:103792/71‑1 (MQ=255)
ggCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTg < 1:1105084/71‑1 (MQ=255)
ggCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTg < 1:1325456/71‑1 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAg > 1:202264/1‑70 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAg > 1:1757362/1‑70 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAg > 1:29483/1‑70 (MQ=255)
ggTTTTTTCTGTATTCATCTCCTGTTTCTTGTTGATTCAATTTCGTTTCacaa < 1:1574615/53‑1 (MQ=255)
tttttCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTgcgc > 1:377069/1‑70 (MQ=255)
tttttCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTgcgc > 1:187508/1‑70 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGGAAGTTGCGCAATCGAATCCGGa > 1:378029/1‑71 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGa > 1:1899255/1‑71 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGa > 1:1710816/1‑71 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGa > 1:1562117/1‑71 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGa > 1:1493277/1‑71 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGa > 1:1374679/1‑71 (MQ=255)
|
ACCAAAGCCTCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGA > W3110S.gb/2893116‑2893237
|
| Alignment Legend |
|---|
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG |
Unaligned base: atcg Masked matching base: atcg Alignment gap: ‑ Deleted base: ‑ |
GATK/CNVnator alignment
N/A
