Resource
| Id | Histone_ChIP-seq/ENCSR461LTR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR461LTR [biosample_summary="Homo sapiens MM.1S" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Released analysis {ENCAN743GUQ|/analyses/ENCAN743GUQ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN743GUQ|/analyses/ENCAN743GUQ/} has in progress subobject document {1290f0f6-66d9-4bec-805d-66c69c14a6fa|/documents/1290f0f6-66d9-4bec-805d-66c69c14a6fa/} audit_not_compliant: Processed unfiltered alignments file {ENCFF776ZIB|/files/ENCFF776ZIB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 31761003 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) 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 {ENCFF193NKB|/files/ENCFF193NKB/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF193NKB|/files/ENCFF193NKB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.22. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR461LTR | float |
Histone_ChIP-seq_ENCSR461LTR |
Histone_ChIP-seq ENCSR461LTR [biosample_summary="Homo sapiens MM.1S" and target="H3K9me3"]
|
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[1.97, 4.56] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 249260 | 0.01% | 715 |
| chr1 | 18898 | 0.01% | 56 |
| chr2 | 21075 | 0.01% | 58 |
| chr3 | 14711 | 0.01% | 45 |
| chr4 | 18731 | 0.01% | 57 |
| chr5 | 14832 | 0.01% | 43 |
| chr6 | 8291 | <0.01% | 23 |
| chr7 | 20398 | 0.01% | 57 |
| chr8 | 11034 | 0.01% | 34 |
| chr9 | 11640 | 0.01% | 31 |
| chr10 | 11294 | 0.01% | 37 |
| chr11 | 13675 | 0.01% | 37 |
| chr12 | 11456 | 0.01% | 32 |
| chr13 | 2913 | <0.01% | 9 |
| chr15 | 8971 | 0.01% | 27 |
| chr16 | 7269 | 0.01% | 21 |
| chr17 | 1789 | <0.01% | 5 |
| chr18 | 7597 | 0.01% | 24 |
| chr19 | 29509 | 0.05% | 72 |
| chr20 | 4650 | 0.01% | 16 |
| chr21 | 5132 | 0.01% | 14 |
| chr22 | 2354 | <0.01% | 7 |
| chrX | 3041 | <0.01% | 10 |
| 3344 contigs with no values (293348218 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 715 | 186 | 1849 | 348.62 | 315 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF853UHY.bed.gz | 15.42 KB | accfdb467967b24ca39b4d0f521a3ffd |
| ENCFF853UHY.tabix.bed.gz | 7.73 KB | af5c4ded554e468bf0a9173ba4cdba8c |
| ENCFF853UHY.tabix.bed.gz.tbi | 11.88 KB | 8cc29f0ff61c5606a7780ee3872aa6b4 |
| genomic_resource.yaml | 3.41 KB | bc0a76fd9c86b09c0aa130158415c944 |
| statistics/ |
