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 |
|
A2 F1 I0 R1
|
4577 |
57.4 |
3436498 |
77.7% |
2670158 |
63.4 |
Breseq alignment
BRESEQ :: Evidence
|
| evidence |
seq id |
position |
mutation |
freq |
annotation |
gene |
description |
| RA |
minE |
1,350,591 |
C→T |
24.9% |
E77E (GAG→GAA) |
dcd ← |
2'‑deoxycytidine 5'‑triphosphate deaminase |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 1,350,591 | 0 | C | T | 24.9%
| 72.9
/ 18.8
| 60 | E77E (GAG→GAA) | dcd | 2'‑deoxycytidine 5'‑triphosphate deaminase |
| Reads supporting (aligned to +/- strand): ref base C (24/21); new base T (9/6); total (33/27) |
| Fisher's exact test for biased strand distribution p-value = 7.68e-01 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.57e-01 |
GTCACCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTGGG > minE/1350529‑1350653
|
gTCACCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCtcg > 1:2636430/1‑66 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:904955/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:1248244/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:63869/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:2682666/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:1590277/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:1634436/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:1693564/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCgaga > 1:2007090/1‑69 (MQ=255)
aCCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCga > 1:386529/1‑67 (MQ=255)
gACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACg < 1:1107370/69‑1 (MQ=255)
gACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACg < 1:2959335/69‑1 (MQ=255)
gACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACg < 1:2081851/69‑1 (MQ=255)
cACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCt < 1:1504929/69‑1 (MQ=255)
cACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCt < 1:2983683/69‑1 (MQ=255)
cACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCt < 1:2553101/69‑1 (MQ=255)
aCCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCt < 1:3190229/68‑1 (MQ=255)
ctctCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAg > 1:2937339/1‑69 (MQ=255)
ctctCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAg > 1:2939417/1‑69 (MQ=255)
ctctCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAg > 1:1429045/1‑69 (MQ=255)
ctctCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAg > 1:2045691/1‑69 (MQ=255)
ctctCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAg > 1:3330433/1‑69 (MQ=255)
ctctCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAg > 1:3016719/1‑69 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAgcgc < 1:287891/67‑1 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAgcgc < 1:1559642/67‑1 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAgcgc < 1:2443360/67‑1 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAgcgc < 1:2185603/67‑1 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAgcgc < 1:3213732/67‑1 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAgcgc < 1:1802445/67‑1 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCgcgg > 1:2993860/1‑69 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCgcgg > 1:3366078/1‑69 (MQ=255)
cTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCgcgg > 1:2887377/1‑69 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCtcatca > 1:1756099/1‑47 (MQ=37)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCa > 1:3031503/1‑68 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCa > 1:910937/1‑68 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCa > 1:981141/1‑68 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCAc > 1:184648/1‑69 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCAc > 1:562511/1‑69 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCAc > 1:1753519/1‑69 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCAc > 1:205677/1‑69 (MQ=255)
aaGATAGAACGCCTCGCTTTCATCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCCCTCAc > 1:2125170/1‑69 (MQ=255)
gATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACtt < 1:461291/69‑1 (MQ=255)
gATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACtt < 1:2100345/69‑1 (MQ=255)
gATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACtt < 1:2104298/69‑1 (MQ=255)
aGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCAt > 1:2671721/1‑69 (MQ=255)
aGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCAt > 1:822151/1‑69 (MQ=255)
aGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCAt > 1:1785707/1‑69 (MQ=255)
aGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCAt > 1:2346122/1‑69 (MQ=255)
aGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCAt > 1:2593445/1‑69 (MQ=255)
aCGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCt < 1:2645630/68‑1 (MQ=255)
aCGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCt < 1:1060566/68‑1 (MQ=255)
aCGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCt < 1:1846446/68‑1 (MQ=255)
gCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCttt < 1:415606/68‑1 (MQ=255)
gCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCttt < 1:2632924/68‑1 (MQ=255)
cTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTggg < 1:2300326/69‑1 (MQ=255)
cTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTggg < 1:3078551/69‑1 (MQ=255)
cTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTggg < 1:3354905/69‑1 (MQ=255)
cTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTggg < 1:2637038/69‑1 (MQ=255)
cTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTggg < 1:2940588/69‑1 (MQ=255)
cTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTggg < 1:1563165/69‑1 (MQ=255)
|
GTCACCGACTCCAGCGTCACCGCCAGCGCCAGCTCTCCTGGGTGAAGATAGAACGCCTCGCCCTCGTCGAGAACGATCTCATCGCTCATCACGCGGTCAAGCGCGGCGCTCACTTCATCTTTGGG > minE/1350529‑1350653
|
| 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
