Resource
| Id | Histone_ChIP-seq/ENCSR128SVE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR128SVE [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (90 or above years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (90 or above years) with Alzheimer's disease output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN281PVN|/analyses/ENCAN281PVN/} 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 {ENCFF497RWO|/files/ENCFF497RWO/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF497RWO|/files/ENCFF497RWO/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.58. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR128SVE | float |
Histone_ChIP-seq_ENCSR128SVE |
Histone_ChIP-seq ENCSR128SVE [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (90 or above years)" and target="H3K4me3"]
|
 |
[1.72, 70.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 78212066 | 2.43% | 50355 |
| chr1 | 7473720 | 3.00% | 4615 |
| chr2 | 5678586 | 2.34% | 3784 |
| chr3 | 4744191 | 2.39% | 2989 |
| chr4 | 3410748 | 1.79% | 2261 |
| chr5 | 4057965 | 2.24% | 2595 |
| chr6 | 4650804 | 2.72% | 3009 |
| chr7 | 3877570 | 2.43% | 2693 |
| chr8 | 3144048 | 2.17% | 2067 |
| chr9 | 3304757 | 2.39% | 2241 |
| chr10 | 3554292 | 2.66% | 2362 |
| chr11 | 4131571 | 3.06% | 2524 |
| chr12 | 4009537 | 3.01% | 2421 |
| chr13 | 1961010 | 1.71% | 1344 |
| chr14 | 2529880 | 2.36% | 1595 |
| chr15 | 2427609 | 2.38% | 1568 |
| chr16 | 2924606 | 3.24% | 1933 |
| chr17 | 4120635 | 4.95% | 2523 |
| chr18 | 1608447 | 2.00% | 1128 |
| chr19 | 4146472 | 7.07% | 2472 |
| chr20 | 1945119 | 3.02% | 1318 |
| chr21 | 828649 | 1.77% | 581 |
| chr22 | 1612374 | 3.17% | 1036 |
| chrX | 2069476 | 1.33% | 1296 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 50355 | 210 | 36259 | 1553.21 | 1010 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF401CRB.bed.gz | 1.23 MB | cec5b74bb94f2dc2841cb30b7533595d |
| ENCFF401CRB.tabix.bed.gz | 558.77 KB | 70b371802ba41be1baf68c4667e8cb25 |
| ENCFF401CRB.tabix.bed.gz.tbi | 251.85 KB | 3b195db650eb5a38bea3e8e733fa65d7 |
| genomic_resource.yaml | 3.01 KB | 7515723f1f17c31801b4ecc8a991e65e |
| statistics/ |