Resource
| Id | Histone_ChIP-seq/ENCSR000DRC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DRC [biosample_summary="Homo sapiens GM12865" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN327RDM|/analyses/ENCAN327RDM/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF447JKC|/files/ENCFF447JKC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14268339 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 {ENCFF575COH|/files/ENCFF575COH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF575COH|/files/ENCFF575COH/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.00. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DRC | float |
Histone_ChIP-seq_ENCSR000DRC |
Histone_ChIP-seq ENCSR000DRC [biosample_summary="Homo sapiens GM12865" and target="H3K4me3"]
|
 |
[1.78, 62.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 43070198 | 1.34% | 35314 |
| chr1 | 4179852 | 1.68% | 3403 |
| chr2 | 3043554 | 1.26% | 2476 |
| chr3 | 2582254 | 1.30% | 2060 |
| chr4 | 1640846 | 0.86% | 1284 |
| chr5 | 2227981 | 1.23% | 1748 |
| chr6 | 2778455 | 1.63% | 2116 |
| chr7 | 2009508 | 1.26% | 1708 |
| chr8 | 1651600 | 1.14% | 1385 |
| chr9 | 1683389 | 1.22% | 1401 |
| chr10 | 1886432 | 1.41% | 1554 |
| chr11 | 2094089 | 1.55% | 1679 |
| chr12 | 2339289 | 1.76% | 1818 |
| chr13 | 937055 | 0.82% | 788 |
| chr14 | 1565152 | 1.46% | 1285 |
| chr15 | 1441819 | 1.41% | 1175 |
| chr16 | 1606794 | 1.78% | 1368 |
| chr17 | 2407766 | 2.89% | 2013 |
| chr18 | 765935 | 0.95% | 646 |
| chr19 | 2457630 | 4.19% | 2115 |
| chr20 | 1055718 | 1.64% | 942 |
| chr21 | 486341 | 1.04% | 417 |
| chr22 | 949485 | 1.87% | 829 |
| chrX | 1278614 | 0.82% | 1103 |
| chrY | 640 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 35314 | 175 | 23187 | 1219.64 | 822 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF573SCA.bed.gz | 916.56 KB | 5644da0597dde0573295bd155c19243d |
| ENCFF573SCA.tabix.bed.gz | 402.13 KB | b1e03c8ccd5f211d267527300239ec08 |
| ENCFF573SCA.tabix.bed.gz.tbi | 160.94 KB | 8f38982cb14f0d673a4eab748322e474 |
| genomic_resource.yaml | 3.46 KB | 9a1c1e2c47acf234f3e96382564c78a4 |
| statistics/ |