Resource
| Id | Histone_ChIP-seq/ENCSR000DQV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DQV [biosample_summary="Homo sapiens GM06990" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN863YUF|/analyses/ENCAN863YUF/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF107KVL|/files/ENCFF107KVL/} processed by ChIP-seq ENCODE3 hg19 pipeline has 10205572 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: Processed alignments file {ENCFF798RRY|/files/ENCFF798RRY/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14133852 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 {ENCFF798RRY|/files/ENCFF798RRY/} 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 {ENCFF798RRY|/files/ENCFF798RRY/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.61. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DQV | float |
Histone_ChIP-seq_ENCSR000DQV |
Histone_ChIP-seq ENCSR000DQV [biosample_summary="Homo sapiens GM06990" and target="H3K4me3"]
|
 |
[1.92, 108] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 37557681 | 1.17% | 35172 |
| chr1 | 3705053 | 1.49% | 3423 |
| chr2 | 2587846 | 1.07% | 2455 |
| chr3 | 2138423 | 1.08% | 1960 |
| chr4 | 1432165 | 0.75% | 1297 |
| chr5 | 1859642 | 1.02% | 1673 |
| chr6 | 2347289 | 1.37% | 2135 |
| chr7 | 1763542 | 1.11% | 1699 |
| chr8 | 1407120 | 0.97% | 1375 |
| chr9 | 1491766 | 1.08% | 1422 |
| chr10 | 1561753 | 1.17% | 1506 |
| chr11 | 1925559 | 1.43% | 1724 |
| chr12 | 2028166 | 1.52% | 1833 |
| chr13 | 786603 | 0.69% | 771 |
| chr14 | 1271810 | 1.19% | 1190 |
| chr15 | 1246992 | 1.22% | 1165 |
| chr16 | 1496939 | 1.66% | 1445 |
| chr17 | 2183976 | 2.62% | 2021 |
| chr18 | 647050 | 0.81% | 657 |
| chr19 | 2365824 | 4.04% | 2223 |
| chr20 | 945147 | 1.47% | 881 |
| chr21 | 402464 | 0.86% | 398 |
| chr22 | 863924 | 1.70% | 842 |
| chrX | 1098035 | 0.70% | 1076 |
| chrY | 593 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 35172 | 145 | 14933 | 1067.83 | 625 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF357ALO.bed.gz | 880.74 KB | 3ec77e0da9f18deedf8843a8ca41af17 |
| ENCFF357ALO.tabix.bed.gz | 391.25 KB | 3f0176335702b6dad5fc1ca02e2ad072 |
| ENCFF357ALO.tabix.bed.gz.tbi | 158.47 KB | c4aedf670d545e928e9fe8aa38e8b742 |
| genomic_resource.yaml | 3.96 KB | b6d44713e9599eab8c3a5a461192d53f |
| statistics/ |