Resource
| Id | Histone_ChIP-seq/ENCSR000DQR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DQR [biosample_summary="Homo sapiens B cell female adult (27 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 3 summary: female adult (27 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN065YTV|/analyses/ENCAN065YTV/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF699RDR|/files/ENCFF699RDR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17181470 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF699RDR|/files/ENCFF699RDR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF699RDR|/files/ENCFF699RDR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.74. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DQR | float |
Histone_ChIP-seq_ENCSR000DQR |
Histone_ChIP-seq ENCSR000DQR [biosample_summary="Homo sapiens B cell female adult (27 years)" and target="H3K4me3"]
|
 |
[1.97, 141] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 35390449 | 1.10% | 28125 |
| chr1 | 3523467 | 1.42% | 2776 |
| chr1_KI270712v1_random | 521 | 0.30% | 1 |
| chr2 | 2443593 | 1.01% | 1977 |
| chr3 | 1915012 | 0.97% | 1516 |
| chr4 | 1281472 | 0.67% | 972 |
| chr5 | 1594459 | 0.88% | 1184 |
| chr6 | 2260666 | 1.32% | 1734 |
| chr7 | 1667143 | 1.05% | 1383 |
| chr8 | 1319857 | 0.91% | 1078 |
| chr9 | 1384790 | 1.00% | 1165 |
| chr10 | 1460095 | 1.09% | 1204 |
| chr11 | 1900627 | 1.41% | 1426 |
| chr12 | 1875133 | 1.41% | 1443 |
| chr13 | 719985 | 0.63% | 586 |
| chr14 | 1196270 | 1.12% | 938 |
| chr15 | 1124072 | 1.10% | 887 |
| chr16 | 1416054 | 1.57% | 1174 |
| chr17 | 2106206 | 2.53% | 1631 |
| chr17_GL000205v2_random | 2116 | 1.14% | 1 |
| chr18 | 563919 | 0.70% | 483 |
| chr19 | 2388392 | 4.07% | 1896 |
| chr20 | 910295 | 1.41% | 757 |
| chr21 | 343768 | 0.74% | 293 |
| chr22 | 846317 | 1.67% | 722 |
| chrUn_GL000219v1 | 3091 | 1.72% | 5 |
| chrUn_GL000220v1 | 342 | 0.21% | 1 |
| chrX | 1142787 | 0.73% | 892 |
| 3339 contigs with no values (185601866 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 28125 | 185 | 12730 | 1258.33 | 1026 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF297YIN.bed.gz | 724.83 KB | 3fc2f6d406a5278f1682d6270a6dbcaf |
| ENCFF297YIN.tabix.bed.gz | 316.24 KB | 78fd8b7612cff5b50c94e3e821a52583 |
| ENCFF297YIN.tabix.bed.gz.tbi | 159.13 KB | 5c8cd04a9e4a5718a6be32214fa4ce84 |
| genomic_resource.yaml | 3.21 KB | 929011c086ac29f39c0e585d613436a7 |
| statistics/ |