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 |
984,663 |
G→A |
39.1% |
D162D (GAC→GAT) |
ynfC ← |
hypothetical protein |
|
| |
seq id |
position |
ref |
new |
freq |
score (cons/poly) |
reads |
annotation |
genes |
product |
| * | minE | 984,663 | 0 | G | A | 39.1%
| 34.9
/ 44.0
| 69 | D162D (GAC→GAT) | ynfC | hypothetical protein |
| Reads supporting (aligned to +/- strand): ref base G (30/12); new base A (12/15); total (42/27) |
| Fisher's exact test for biased strand distribution p-value = 4.23e-02 |
| Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.61e-01 |
TAACCGCTGTGTAATCTAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCATC > minE/984596‑984723
|
taaCCGCTGTGTAATCTAATTTTTTGATCTGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGt > 1:1686348/1‑69 (MQ=255)
aCCGCTGTGTAATCTAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTc > 1:2166048/1‑68 (MQ=255)
aCCGCTGTGTAATCTAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTc > 1:890417/1‑68 (MQ=255)
aCCGCTGTGTAATCTAATTTTTTGATAGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTc > 1:1296715/1‑68 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:950533/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:2058663/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:2237931/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:1446309/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:503752/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:3327726/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:138854/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:2787306/68‑1 (MQ=255)
tAATCTAATTTTTTGATCGGGTCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACtttt < 1:2949284/68‑1 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGGTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:1935898/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:3290011/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:394542/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:2707614/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:3341025/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:3373670/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:2067715/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:1963588/1‑69 (MQ=255)
tAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGt > 1:2031239/1‑69 (MQ=255)
ccGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:472712/69‑1 (MQ=255)
ccGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:2881195/69‑1 (MQ=255)
ccGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:1625734/69‑1 (MQ=255)
ccGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:1161890/69‑1 (MQ=255)
ccGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:1394449/69‑1 (MQ=255)
ccGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:1194690/69‑1 (MQ=255)
ccGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:1357764/69‑1 (MQ=255)
gATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:958790/64‑1 (MQ=255)
gATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCTGCGGATACCCCTGa < 1:3195049/69‑1 (MQ=255)
gATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCGGATACCCCTGa < 1:1615745/69‑1 (MQ=255)
gATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCGGATACCCCTGa < 1:1529648/69‑1 (MQ=255)
gATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCGGATACCCCTGa < 1:2848222/69‑1 (MQ=255)
gATGGCGTGGCGCTGACAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCGGATACCCCTGa < 1:589788/69‑1 (MQ=255)
tggcgtggcgCTGACAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCGGATACCCCTGa < 1:2473206/67‑1 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCTTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:737454/1‑67 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:871173/1‑67 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:1202216/1‑67 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:2440137/1‑67 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:1015647/1‑67 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:1446910/1‑67 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:1871906/1‑67 (MQ=255)
gtggcgCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACACTGatcat > 1:2180456/1‑67 (MQ=255)
gtggcgATGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCa > 1:1419596/1‑49 (MQ=255)
gtggagCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGatcat > 1:1104295/1‑67 (MQ=255)
gcgcTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATa > 1:757185/1‑68 (MQ=255)
gcgcTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATa > 1:1827949/1‑68 (MQ=255)
gcgcTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATa > 1:1515680/1‑68 (MQ=255)
aCAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAAc < 1:2616058/49‑1 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:845612/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:865155/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:943538/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:994625/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:3214421/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:3075953/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:2552752/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:2513733/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:2511382/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:2434947/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:2306638/1‑42 (MQ=255)
cAGATAATGTTTTATCGTTACTTTTCGTGGTTTTACCCAGCg > 1:2065426/1‑42 (MQ=255)
aTAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCTTAGCGATATTCCa < 1:2336195/69‑1 (MQ=255)
aTAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCa < 1:540805/69‑1 (MQ=255)
aTAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCa < 1:310355/69‑1 (MQ=255)
aaTGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCAt > 1:420981/1‑68 (MQ=255)
aaTGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCATc > 1:472367/1‑69 (MQ=255)
aaTGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCATc > 1:841793/1‑69 (MQ=255)
aaTGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCATc > 1:1368573/1‑69 (MQ=255)
|
TAACCGCTGTGTAATCTAATTTTTTGATCGGATCCGTTGATGGCGTGGCGCTGACAGATAATGTTTTGTCGTTACTTTTCGTGGTTTTACCCAGCGGATAACCCTGATCATCATAGCGATATTCCATC > minE/984596‑984723
|
| 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
