Resource
| Id | Histone_ChIP-seq/ENCSR199KHR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR199KHR [biosample_summary="Homo sapiens OCI-LY7" and target="H3K9me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN590NSV|/analyses/ENCAN590NSV/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF427SFL|/files/ENCFF427SFL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 18379693 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me2-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 {ENCFF427SFL|/files/ENCFF427SFL/} 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 {ENCFF427SFL|/files/ENCFF427SFL/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.44. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR199KHR | float |
Histone_ChIP-seq_ENCSR199KHR |
Histone_ChIP-seq ENCSR199KHR [biosample_summary="Homo sapiens OCI-LY7" and target="H3K9me2"]
|
 |
[1.48, 4.41] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 1228952 | 0.04% | 3508 |
| chr1 | 93532 | 0.04% | 266 |
| chr2 | 113565 | 0.05% | 327 |
| chr3 | 109628 | 0.06% | 315 |
| chr4 | 94153 | 0.05% | 277 |
| chr5 | 104895 | 0.06% | 302 |
| chr6 | 82785 | 0.05% | 242 |
| chr7 | 63322 | 0.04% | 187 |
| chr8 | 71002 | 0.05% | 207 |
| chr9 | 48480 | 0.04% | 149 |
| chr10 | 51074 | 0.04% | 143 |
| chr11 | 54894 | 0.04% | 162 |
| chr12 | 62861 | 0.05% | 183 |
| chr13 | 113415 | 0.10% | 286 |
| chr14 | 45029 | 0.04% | 124 |
| chr15 | 27756 | 0.03% | 77 |
| chr16 | 19553 | 0.02% | 54 |
| chr17 | 23471 | 0.03% | 64 |
| chr17_GL000205v2_random | 364 | 0.20% | 1 |
| chr18 | 10273 | 0.01% | 30 |
| chr19 | 4862 | 0.01% | 15 |
| chr20 | 17068 | 0.03% | 50 |
| chr21 | 13293 | 0.03% | 36 |
| chr22 | 3207 | 0.01% | 10 |
| chrX | 470 | <0.01% | 1 |
| 3342 contigs with no values (186118909 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 3508 | 195 | 1274 | 350.33 | 326 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF601CVT.bed.gz | 70.2 KB | 0b742051c3caee4bd7cc86c5901f9b6f |
| ENCFF601CVT.tabix.bed.gz | 36.61 KB | 0a39e095bc6997cd0faf9defec55bbc5 |
| ENCFF601CVT.tabix.bed.gz.tbi | 38.48 KB | 59f262457fef3fbe25efd54c83571553 |
| genomic_resource.yaml | 3.17 KB | 9d37c72ba59e66a7dfe608a1e393078e |
| statistics/ |