Resource
| Id | Histone_ChIP-seq/ENCSR548QRE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR548QRE [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (81 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (81 years) with Alzheimer's disease output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN295LBP|/analyses/ENCAN295LBP/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.8 is acceptable. ENCODE processed alignments file {ENCFF276EMZ|/files/ENCFF276EMZ/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed alignments file {ENCFF276EMZ|/files/ENCFF276EMZ/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR548QRE | float |
Histone_ChIP-seq_ENCSR548QRE |
Histone_ChIP-seq ENCSR548QRE [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (81 years)" and target="H3K4me3"]
|
 |
[1.69, 60.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 68239471 | 2.12% | 35020 |
| chr1 | 6602133 | 2.65% | 3313 |
| chr2 | 4756179 | 1.96% | 2496 |
| chr3 | 4066333 | 2.05% | 2013 |
| chr4 | 2869150 | 1.51% | 1505 |
| chr5 | 3498112 | 1.93% | 1770 |
| chr6 | 4033495 | 2.36% | 2097 |
| chr7 | 3348818 | 2.10% | 1831 |
| chr8 | 2708011 | 1.87% | 1412 |
| chr9 | 2815411 | 2.03% | 1491 |
| chr10 | 3019415 | 2.26% | 1602 |
| chr11 | 3652271 | 2.70% | 1772 |
| chr12 | 3607624 | 2.71% | 1738 |
| chr13 | 1660358 | 1.45% | 916 |
| chr14 | 2157217 | 2.02% | 1092 |
| chr15 | 2125884 | 2.08% | 1099 |
| chr16 | 2569087 | 2.84% | 1343 |
| chr17 | 3651870 | 4.39% | 1792 |
| chr18 | 1315200 | 1.64% | 725 |
| chr19 | 3903780 | 6.66% | 1996 |
| chr20 | 1740085 | 2.70% | 894 |
| chr21 | 708556 | 1.52% | 402 |
| chr22 | 1485471 | 2.92% | 738 |
| chrX | 1945011 | 1.25% | 983 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 35020 | 258 | 35186 | 1948.59 | 1413 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF154JNK.bed.gz | 915.63 KB | 77b850f60d4e729ae7283bed25c0a7cc |
| ENCFF154JNK.tabix.bed.gz | 399.9 KB | f6d69a41b1e915c28d1b1c376d10af58 |
| ENCFF154JNK.tabix.bed.gz.tbi | 207.03 KB | d42d291bf962802d0a573f9eb7602166 |
| genomic_resource.yaml | 2.97 KB | ef0385fe335de9ba552f796a252f7870 |
| statistics/ |