Resource
| Id | Histone_ChIP-seq/ENCSR817LUF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR817LUF [biosample_summary="Homo sapiens brain tissue female embryo (120 days)" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (120 days) output_type: pseudoreplicated peaks audit_internal_action: Released file {ENCFF803UAK|/files/ENCFF803UAK/} has revoked subobject file {ENCFF445RZC|/files/ENCFF445RZC/} audit_internal_action: Released analysis {ENCAN622WHH|/analyses/ENCAN622WHH/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF465HGP|/files/ENCFF465HGP/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 27081532 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: The md5 sum of file {ENCFF803UAK|/files/ENCFF803UAK/} matches that of file(s) {ENCFF445RZC|/files/ENCFF445RZC/}. 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 {ENCFF465HGP|/files/ENCFF465HGP/} processed by ChIP-seq ENCODE4 v1.8.1 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 {ENCFF465HGP|/files/ENCFF465HGP/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.71. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR817LUF | float |
Histone_ChIP-seq_ENCSR817LUF |
Histone_ChIP-seq ENCSR817LUF [biosample_summary="Homo sapiens brain tissue female embryo (120 days)" and target="H3K36me3"]
|
 |
[1.81, 33.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 60630832 | 1.88% | 96255 |
| chr1 | 6510730 | 2.62% | 10063 |
| chr2 | 4248029 | 1.75% | 7263 |
| chr3 | 3184198 | 1.61% | 5329 |
| chr4 | 1965200 | 1.03% | 3411 |
| chr5 | 2746374 | 1.51% | 4614 |
| chr6 | 2376669 | 1.39% | 4021 |
| chr7 | 2899091 | 1.82% | 4795 |
| chr8 | 1841780 | 1.27% | 3135 |
| chr9 | 2650738 | 1.92% | 4096 |
| chr10 | 2329358 | 1.74% | 3972 |
| chr11 | 3486276 | 2.58% | 5324 |
| chr12 | 3510744 | 2.63% | 5378 |
| chr13 | 932740 | 0.82% | 1736 |
| chr14 | 1939356 | 1.81% | 3214 |
| chr15 | 1969350 | 1.93% | 3200 |
| chr16 | 3011720 | 3.33% | 4493 |
| chr17 | 3891476 | 4.67% | 5859 |
| chr18 | 842845 | 1.05% | 1559 |
| chr19 | 4932805 | 8.42% | 6517 |
| chr20 | 2049583 | 3.18% | 3202 |
| chr21 | 759581 | 1.63% | 1203 |
| chr22 | 2058765 | 4.05% | 2976 |
| chrX | 493424 | 0.32% | 895 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 96255 | 260 | 13557 | 629.9 | 480 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF803UAK.bed.gz | 1.75 MB | a049e9b624a17abbf8140587e4b72b81 |
| ENCFF803UAK.tabix.bed.gz | 930.8 KB | ec0a8c50f8a2a03f44dcdd9cbd6ecb11 |
| ENCFF803UAK.tabix.bed.gz.tbi | 201.26 KB | cea25e830269f27ba7def11a2a9f754c |
| genomic_resource.yaml | 3.63 KB | f1d7ae210cdbc3467b24e4cc3f524fa1 |
| statistics/ |