Resource
| Id | Histone_ChIP-seq/ENCSR000ASL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ASL [biosample_summary="Homo sapiens CD14-positive monocyte female" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN630KJZ|/analyses/ENCAN630KJZ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF466TKD|/files/ENCFF466TKD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 14831903 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 {ENCFF704VKY|/files/ENCFF704VKY/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17562040 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 {ENCFF466TKD|/files/ENCFF466TKD/} processed by ChIP-seq ENCODE3 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 {ENCFF466TKD|/files/ENCFF466TKD/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.10. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ASL | float |
Histone_ChIP-seq_ENCSR000ASL |
Histone_ChIP-seq ENCSR000ASL [biosample_summary="Homo sapiens CD14-positive monocyte female" and target="H3K36me3"]
|
 |
[1.74, 38.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 207986180 | 6.46% | 122819 |
| chr1 | 20288074 | 8.15% | 11818 |
| chr2 | 16882532 | 6.97% | 10004 |
| chr3 | 13719277 | 6.92% | 8185 |
| chr4 | 9087413 | 4.78% | 5678 |
| chr5 | 11604152 | 6.39% | 6759 |
| chr6 | 9673558 | 5.66% | 6315 |
| chr7 | 10127813 | 6.36% | 6423 |
| chr8 | 7488691 | 5.16% | 4504 |
| chr9 | 8772645 | 6.34% | 4979 |
| chr10 | 9388226 | 7.02% | 5738 |
| chr11 | 10269817 | 7.60% | 5680 |
| chr12 | 11501172 | 8.63% | 6666 |
| chr13 | 4672407 | 4.09% | 2896 |
| chr14 | 7097270 | 6.63% | 4067 |
| chr15 | 7915717 | 7.76% | 4452 |
| chr16 | 8629314 | 9.55% | 4734 |
| chr17 | 10734712 | 12.89% | 5990 |
| chr18 | 3742848 | 4.66% | 2377 |
| chr19 | 8675002 | 14.80% | 5153 |
| chr20 | 6127968 | 9.51% | 3225 |
| chr21 | 2550542 | 5.46% | 1365 |
| chr22 | 4792757 | 9.43% | 2466 |
| chrUn_GL000219v1 | 254 | 0.14% | 1 |
| chrX | 4244019 | 2.72% | 3344 |
| 3342 contigs with no values (186125302 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 122819 | 240 | 51814 | 1693.44 | 961 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF399HUL.bed.gz | 2.73 MB | 6e602c49421b1f975ff294b0a1dfba72 |
| ENCFF399HUL.tabix.bed.gz | 1.25 MB | c7eaf2c5e5898e3b97cf11f7c3674138 |
| ENCFF399HUL.tabix.bed.gz.tbi | 139.14 KB | 077fa7b5b980b5b7ce83c876101b8b5e |
| genomic_resource.yaml | 3.66 KB | 0714b65884c534edf54d277301657357 |
| statistics/ |