Resource
| Id | Histone_ChIP-seq/ENCSR339TAQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR339TAQ [biosample_summary="Homo sapiens with Alzheimer''s disease, Cognitive impairment; dorsolateral prefrontal cortex tissue male adult (87 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (87 years) with Alzheimer's disease, Cognitive impairment output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN686STI|/analyses/ENCAN686STI/} 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 {ENCFF002UFI|/files/ENCFF002UFI/} 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 {ENCFF002UFI|/files/ENCFF002UFI/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.40. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR339TAQ | float |
Histone_ChIP-seq_ENCSR339TAQ |
Histone_ChIP-seq ENCSR339TAQ [biosample_summary="Homo sapiens with Alzheimer''s disease, Cognitive impairment; dorsolateral prefrontal cortex tissue male adult (87 years)" and target="H3K4me3"]
|
 |
[1.95, 92.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 56158585 | 1.75% | 32044 |
| chr1 | 5472832 | 2.20% | 3047 |
| chr2 | 3887903 | 1.61% | 2245 |
| chr3 | 3323032 | 1.68% | 1806 |
| chr4 | 2330278 | 1.23% | 1326 |
| chr5 | 2840276 | 1.56% | 1616 |
| chr6 | 3291183 | 1.93% | 1911 |
| chr7 | 2731455 | 1.71% | 1664 |
| chr8 | 2242841 | 1.55% | 1295 |
| chr9 | 2293633 | 1.66% | 1368 |
| chr10 | 2441706 | 1.82% | 1422 |
| chr11 | 2999439 | 2.22% | 1625 |
| chr12 | 2999084 | 2.25% | 1637 |
| chr13 | 1331264 | 1.16% | 805 |
| chr14 | 1768254 | 1.65% | 995 |
| chr15 | 1752251 | 1.72% | 1020 |
| chr16 | 2127879 | 2.36% | 1247 |
| chr17 | 3021426 | 3.63% | 1663 |
| chr18 | 1056101 | 1.31% | 621 |
| chr19 | 3309889 | 5.65% | 1913 |
| chr20 | 1441728 | 2.24% | 829 |
| chr21 | 560209 | 1.20% | 345 |
| chr22 | 1229551 | 2.42% | 687 |
| chrX | 1651097 | 1.06% | 927 |
| chrY | 55274 | 0.10% | 30 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 32044 | 195 | 24598 | 1752.55 | 1339 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF038YCT.bed.gz | 825.58 KB | 045d6c26c38e922409ea6cc8b54a1635 |
| ENCFF038YCT.tabix.bed.gz | 364.43 KB | f6828e15d7845dc6a8e9c0896cd81bcf |
| ENCFF038YCT.tabix.bed.gz.tbi | 194.85 KB | ef13018a6d66da94b1c502c663d021be |
| genomic_resource.yaml | 3.07 KB | 918d37bc7ef694372378607743b78955 |
| statistics/ |