Resource
| Id | Histone_ChIP-seq/ENCSR473TDG |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR473TDG [biosample_summary="Homo sapiens Karpas-422" and target="H3K9me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN453LUD|/analyses/ENCAN453LUD/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF938RGB|/files/ENCFF938RGB/} processed by ChIP-seq ENCODE3 hg19 pipeline has 15088592 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_not_compliant: Processed alignments file {ENCFF691ZTN|/files/ENCFF691ZTN/} processed by ChIP-seq ENCODE3 hg19 pipeline has 20500287 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 {ENCFF938RGB|/files/ENCFF938RGB/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF938RGB|/files/ENCFF938RGB/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.16. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR473TDG | float |
Histone_ChIP-seq_ENCSR473TDG |
Histone_ChIP-seq ENCSR473TDG [biosample_summary="Homo sapiens Karpas-422" and target="H3K9me2"]
|
 |
[1.72, 6.44] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 2249411 | 0.07% | 5972 |
| chr1 | 121176 | 0.05% | 327 |
| chr2 | 233754 | 0.10% | 627 |
| chr3 | 198416 | 0.10% | 532 |
| chr4 | 213328 | 0.11% | 545 |
| chr5 | 150296 | 0.08% | 419 |
| chr6 | 128533 | 0.08% | 335 |
| chr7 | 108271 | 0.07% | 296 |
| chr8 | 102791 | 0.07% | 288 |
| chr9 | 64568 | 0.05% | 182 |
| chr10 | 55531 | 0.04% | 151 |
| chr11 | 238853 | 0.18% | 561 |
| chr12 | 96306 | 0.07% | 271 |
| chr13 | 66097 | 0.06% | 188 |
| chr14 | 156395 | 0.15% | 396 |
| chr15 | 26211 | 0.03% | 76 |
| chr16 | 36527 | 0.04% | 97 |
| chr17 | 20481 | 0.02% | 55 |
| chr18 | 103843 | 0.13% | 272 |
| chr19 | 9854 | 0.02% | 25 |
| chr20 | 20480 | 0.03% | 52 |
| chr21 | 13490 | 0.03% | 38 |
| chr22 | 5558 | 0.01% | 17 |
| chrX | 78652 | 0.05% | 222 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 5972 | 195 | 1159 | 376.66 | 347 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF891APA.bed.gz | 117.54 KB | ad0ddb14ac72c8eb9a1d850f790a041c |
| ENCFF891APA.tabix.bed.gz | 61.31 KB | 6338854b07e6b16de1ee85f67662e474 |
| ENCFF891APA.tabix.bed.gz.tbi | 55.75 KB | 8c4b4ff0131a4afc28f5b5e7d27003d5 |
| genomic_resource.yaml | 3.68 KB | 5c58abeadf7fe12670484e27708788f1 |
| statistics/ |