Resource
| Id | Histone_ChIP-seq/ENCSR869WSC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR869WSC [biosample_summary="Homo sapiens brain tissue female embryo (17 weeks)" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (17 weeks) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN989GUL|/analyses/ENCAN989GUL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF558KPT|/files/ENCFF558KPT/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19722554 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 redacted alignments file {ENCFF631IHS|/files/ENCFF631IHS/} processed by ChIP-seq ENCODE3 hg19 pipeline has 33992837 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 redacted alignments file {ENCFF558KPT|/files/ENCFF558KPT/} processed by ChIP-seq ENCODE3 hg19 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 redacted alignments file {ENCFF558KPT|/files/ENCFF558KPT/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.28. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR869WSC | float |
Histone_ChIP-seq_ENCSR869WSC |
Histone_ChIP-seq ENCSR869WSC [biosample_summary="Homo sapiens brain tissue female embryo (17 weeks)" and target="H3K36me3"]
|
 |
[1.41, 16.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 121762283 | 3.78% | 153168 |
| chr1 | 12439032 | 5.00% | 15555 |
| chr2 | 8583100 | 3.54% | 12247 |
| chr3 | 6931544 | 3.50% | 9509 |
| chr4 | 4089875 | 2.15% | 5930 |
| chr5 | 5411258 | 2.98% | 7606 |
| chr6 | 4590449 | 2.69% | 6537 |
| chr7 | 5861396 | 3.68% | 7567 |
| chr8 | 3653505 | 2.52% | 5220 |
| chr9 | 5298206 | 3.83% | 6364 |
| chr10 | 4700282 | 3.51% | 6468 |
| chr11 | 6713184 | 4.97% | 7891 |
| chr12 | 6813151 | 5.11% | 8194 |
| chr13 | 2001365 | 1.75% | 3276 |
| chr14 | 4111304 | 3.84% | 5602 |
| chr15 | 4276771 | 4.19% | 5824 |
| chr16 | 6132170 | 6.79% | 6345 |
| chr17 | 7661942 | 9.20% | 8428 |
| chr18 | 1809492 | 2.25% | 2819 |
| chr19 | 9556975 | 16.30% | 8704 |
| chr20 | 4198140 | 6.51% | 4876 |
| chr21 | 1607119 | 3.44% | 1879 |
| chr22 | 4077299 | 8.02% | 4109 |
| chrX | 1242536 | 0.80% | 2214 |
| chrY | 2188 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 153168 | 200 | 32134 | 794.96 | 495.5 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF713YWB.bed.gz | 2.75 MB | d83c962505dc78f0f8d3c6bbca7a4166 |
| ENCFF713YWB.tabix.bed.gz | 1.43 MB | 4219eddbaea0dad2be52bfafd10ec6b7 |
| ENCFF713YWB.tabix.bed.gz.tbi | 184.46 KB | d9e2aff764046f221e4cbad26b0b08e1 |
| genomic_resource.yaml | 3.75 KB | 4e5a783fe5cfcea915ad8b68baf9f69e |
| statistics/ |