Resource
| Id | Histone_ChIP-seq/ENCSR000EWZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000EWZ [biosample_summary="Homo sapiens NT2/D1" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN806DXS|/analyses/ENCAN806DXS/} has in progress subobject document {a78e9e75-ece9-419f-9b5b-48535982e81e|/documents/a78e9e75-ece9-419f-9b5b-48535982e81e/} audit_internal_action: Released analysis {ENCAN806DXS|/analyses/ENCAN806DXS/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF880VYO|/files/ENCFF880VYO/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 30749371 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 {ENCFF951QES|/files/ENCFF951QES/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF951QES|/files/ENCFF951QES/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.24. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000EWZ | float |
Histone_ChIP-seq_ENCSR000EWZ |
Histone_ChIP-seq ENCSR000EWZ [biosample_summary="Homo sapiens NT2/D1" and target="H3K9me3"]
|
 |
[1.59, 25.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 73456454 | 2.28% | 67772 |
| chr1 | 7448150 | 2.99% | 6544 |
| chr2 | 6452568 | 2.66% | 6077 |
| chr3 | 5949896 | 3.00% | 5557 |
| chr4 | 3794974 | 2.00% | 3613 |
| chr5 | 3289517 | 1.81% | 3309 |
| chr6 | 2941013 | 1.72% | 3017 |
| chr7 | 4044155 | 2.54% | 3695 |
| chr8 | 3771115 | 2.60% | 3546 |
| chr9 | 3531699 | 2.55% | 3167 |
| chr10 | 2676210 | 2.00% | 2612 |
| chr11 | 3015549 | 2.23% | 2881 |
| chr12 | 5243532 | 3.93% | 4546 |
| chr13 | 1314362 | 1.15% | 1402 |
| chr14 | 1727990 | 1.61% | 1679 |
| chr15 | 1942545 | 1.90% | 1842 |
| chr16 | 2576085 | 2.85% | 2284 |
| chr17 | 1857264 | 2.23% | 1726 |
| chr18 | 1359162 | 1.69% | 1343 |
| chr19 | 4137826 | 7.06% | 2671 |
| chr20 | 1586475 | 2.46% | 1516 |
| chr21 | 1535261 | 3.29% | 1342 |
| chr22 | 721384 | 1.42% | 704 |
| chrX | 2425169 | 1.55% | 2558 |
| chrY | 114553 | 0.20% | 141 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 67772 | 238 | 34123 | 1083.88 | 825 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF062IAJ.bed.gz | 1.44 MB | 54fd918054b460b26645c304439e5710 |
| ENCFF062IAJ.tabix.bed.gz | 702.41 KB | bd71b7713b3d99bc7e4b7bc622f1564f |
| ENCFF062IAJ.tabix.bed.gz.tbi | 314.31 KB | a09202a897fdbc313dbd4e77d69f41e6 |
| genomic_resource.yaml | 3.42 KB | 6dc84e6e8c158fe58eb5fdd068d177b6 |
| statistics/ |