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 F17 I0 R2
|
276 |
45.3 |
3729697 |
93.0% |
3468618 |
60.6 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
W3110S.gb |
2,893,179 |
A→C |
24.6% |
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 | 24.6%
| 49.6
/ 44.2
| 53 | I110L (ATT→CTT) | ygcP | predicted anti‑terminator regulatory protein |
| Reads supporting (aligned to +/- strand): ref base A (23/17); new base C (9/4); total (32/21) |
| Fisher's exact test for biased strand distribution p-value = 5.29e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 2.27e-01 |
AGTACCAAAGCCTCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGTA > W3110S.gb/2893113‑2893242
|
aGTACCAAAGCCTCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCtt < 1:1139451/69‑1 (MQ=255)
aCCAAAGCCTCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTAttgtt < 1:3175989/69‑1 (MQ=255)
tCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAAtt < 1:2846930/69‑1 (MQ=255)
aGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCacaa > 1:2041376/1‑69 (MQ=255)
aGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCacaa > 1:1643039/1‑69 (MQ=255)
aGCGGCAAGAGCGGAAGGTTTTTTCTGTATTAATCGCCTGTTTATTGTTGATTCAATTTCGTTTCacaa > 1:3399216/1‑69 (MQ=255)
gCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACAtt > 1:3519099/1‑69 (MQ=255)
cAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTg < 1:3463831/69‑1 (MQ=255)
aaGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGa < 1:3199650/69‑1 (MQ=255)
aaGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGa < 1:1784726/69‑1 (MQ=255)
agagCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGa < 1:460948/68‑1 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATa > 1:690984/1‑68 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATa > 1:1070587/1‑68 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGt > 1:1737430/1‑53 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGt > 1:300038/1‑53 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGt > 1:1168545/1‑53 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGt > 1:2545716/1‑53 (MQ=255)
agCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGt > 1:2622860/1‑53 (MQ=255)
cGGAAGGTTTTTTCTGTATTCATCGCCTGTTTCtt < 1:2620151/35‑1 (MQ=255)
ggAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCa < 1:2059055/69‑1 (MQ=255)
ggAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCa < 1:162021/69‑1 (MQ=255)
ggAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCa < 1:3610723/69‑1 (MQ=255)
ggAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCa < 1:2525023/69‑1 (MQ=255)
gAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCa < 1:1727057/68‑1 (MQ=255)
gTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCa < 1:2788620/38‑1 (MQ=255)
gTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCa < 1:2411560/38‑1 (MQ=255)
tttttCTGTATTCATCGCCTGTTTCTTGTTGATTCAATTTCg > 1:3691803/1‑42 (MQ=255)
tttttCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCacaa > 1:858530/1‑50 (MQ=255)
tttttCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCacaa > 1:1829893/1‑50 (MQ=255)
tttCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCa > 1:2460422/1‑69 (MQ=255)
tttCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCa > 1:3694046/1‑69 (MQ=255)
tttCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCa > 1:1388199/1‑69 (MQ=255)
ttCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTgcgc > 1:3298800/1‑60 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCg > 1:3686750/1‑69 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCg > 1:39514/1‑69 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCg > 1:3437023/1‑69 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCg > 1:3121132/1‑69 (MQ=255)
cATCGCCTGTTTCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCg > 1:1309547/1‑69 (MQ=255)
cATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTg < 1:91050/43‑1 (MQ=255)
cATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTg < 1:2189090/43‑1 (MQ=255)
cATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTg < 1:1284781/43‑1 (MQ=255)
cATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCg > 1:1579400/1‑69 (MQ=255)
cTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGt > 1:3122004/1‑69 (MQ=255)
cTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGt > 1:3094501/1‑69 (MQ=255)
cTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGt > 1:2449660/1‑69 (MQ=255)
cTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGt < 1:805730/69‑1 (MQ=255)
tGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGt < 1:235491/68‑1 (MQ=255)
tttCTTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGTa > 1:1000065/1‑67 (MQ=255)
tATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGGAATCGAATCCGGATTGTa > 1:2203078/1‑65 (MQ=255)
tATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCa > 1:2076045/1‑48 (MQ=255)
tATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGTa > 1:2580120/1‑65 (MQ=255)
tATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGTa > 1:100451/1‑65 (MQ=255)
tATTGTTGATTCAATTTCGTTT‑‑CAACATTGATAAGc < 1:2336330/36‑1 (MQ=37)
|
AGTACCAAAGCCTCAATGTTGAAAGCGGCAAGAGCGGAAGGTTTTTTCTGTATTCATCGCCTGTTTATTGTTGATTCAATTTCGTTTCACAACATTGATAAGCAAGTTGCGCAATCGAATCCGGATTGTA > W3110S.gb/2893113‑2893242
|
| 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
