Resource
| Id | Histone_ChIP-seq/ENCSR000DWW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DWW [biosample_summary="Homo sapiens keratinocyte female" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN354SXS|/analyses/ENCAN354SXS/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF418GTR|/files/ENCFF418GTR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10909346 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_not_compliant: Processed alignments file {ENCFF352EMC|/files/ENCFF352EMC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 10848734 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: 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 {ENCFF418GTR|/files/ENCFF418GTR/} processed by ChIP-seq ENCODE3 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 {ENCFF418GTR|/files/ENCFF418GTR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.08. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DWW | float |
Histone_ChIP-seq_ENCSR000DWW |
Histone_ChIP-seq ENCSR000DWW [biosample_summary="Homo sapiens keratinocyte female" and target="H3K36me3"]
|
 |
[1.87, 13] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 46250244 | 1.44% | 162119 |
| chr1 | 4770174 | 1.92% | 16495 |
| chr1_KI270711v1_random | 229 | 0.54% | 1 |
| chr2 | 3135556 | 1.29% | 11656 |
| chr3 | 2675023 | 1.35% | 9491 |
| chr4 | 1631417 | 0.86% | 6284 |
| chr5 | 2169023 | 1.19% | 7872 |
| chr6 | 1913587 | 1.12% | 7012 |
| chr7 | 2046641 | 1.28% | 7419 |
| chr8 | 1595441 | 1.10% | 5907 |
| chr9 | 2012243 | 1.45% | 6948 |
| chr9_KI270718v1_random | 187 | 0.49% | 1 |
| chr10 | 1949389 | 1.46% | 6921 |
| chr11 | 2596045 | 1.92% | 8879 |
| chr12 | 2584824 | 1.94% | 8952 |
| chr13 | 731162 | 0.64% | 2838 |
| chr14 | 1494777 | 1.40% | 5294 |
| chr15 | 1580335 | 1.55% | 5734 |
| chr16 | 2353840 | 2.61% | 7888 |
| chr17 | 2993872 | 3.60% | 9810 |
| chr18 | 761707 | 0.95% | 2908 |
| chr19 | 2933984 | 5.01% | 9336 |
| chr20 | 1630154 | 2.53% | 5350 |
| chr21 | 648793 | 1.39% | 2189 |
| chr22 | 1620680 | 3.19% | 5172 |
| chrUn_KI270466v1 | 128 | 10.38% | 1 |
| chrUn_KI270467v1 | 250 | 6.38% | 1 |
| chrX | 420783 | 0.27% | 1760 |
| 3339 contigs with no values (186219083 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 162119 | 125 | 5607 | 285.29 | 224 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF270RNZ.bed.gz | 2.78 MB | 80813560e2dd7fa7494bdf723a27c8f4 |
| ENCFF270RNZ.tabix.bed.gz | 1.45 MB | f16aea3703a53f7b76678395728e85b0 |
| ENCFF270RNZ.tabix.bed.gz.tbi | 208.48 KB | 4bbc1f2eb5177192c641fcc8ef5e965d |
| genomic_resource.yaml | 3.93 KB | 4473d9a190d8fdf0646cb81df3a9b20f |
| statistics/ |