Resource
| Id | Histone_ChIP-seq/ENCSR857HWF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR857HWF [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 {ENCAN124SSU|/analyses/ENCAN124SSU/} 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 {ENCFF941TUE|/files/ENCFF941TUE/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF941TUE|/files/ENCFF941TUE/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 7.32. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR857HWF | float |
Histone_ChIP-seq_ENCSR857HWF |
Histone_ChIP-seq ENCSR857HWF [biosample_summary="Homo sapiens with Alzheimer''s disease; dorsolateral prefrontal cortex tissue female adult (90 or above years)" and target="H3K4me3"]
|
 |
[1.75, 77.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 73174389 | 2.27% | 45279 |
| chr1 | 7039385 | 2.83% | 4227 |
| chr2 | 5205538 | 2.15% | 3335 |
| chr3 | 4316941 | 2.18% | 2658 |
| chr4 | 3053437 | 1.61% | 1951 |
| chr5 | 3791262 | 2.09% | 2367 |
| chr6 | 4200900 | 2.46% | 2657 |
| chr7 | 3618988 | 2.27% | 2366 |
| chr8 | 2944359 | 2.03% | 1896 |
| chr9 | 3046086 | 2.20% | 1921 |
| chr10 | 3229320 | 2.41% | 2079 |
| chr11 | 3907023 | 2.89% | 2262 |
| chr12 | 3833484 | 2.88% | 2242 |
| chr13 | 1769604 | 1.55% | 1207 |
| chr14 | 2309211 | 2.16% | 1421 |
| chr15 | 2291793 | 2.25% | 1438 |
| chr16 | 2792800 | 3.09% | 1763 |
| chr17 | 3928036 | 4.72% | 2318 |
| chr18 | 1433419 | 1.78% | 955 |
| chr19 | 4142624 | 7.07% | 2401 |
| chr20 | 1907814 | 2.96% | 1193 |
| chr21 | 743336 | 1.59% | 510 |
| chr22 | 1634247 | 3.22% | 945 |
| chrX | 2034494 | 1.30% | 1166 |
| chrY | 288 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 45279 | 190 | 35325 | 1616.08 | 1007 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF714WHK.bed.gz | 1.1 MB | 583bb8493167cac5432251ddb9a1dd87 |
| ENCFF714WHK.tabix.bed.gz | 502.37 KB | 4e410461044103d6bd334dc347b72161 |
| ENCFF714WHK.tabix.bed.gz.tbi | 237.01 KB | bbb4baedf272c062abcead3659c822dc |
| genomic_resource.yaml | 3.01 KB | ef7efa73776496593da3fe4bac6621ed |
| statistics/ |