Resource
| Id | Histone_ChIP-seq/ENCSR333ZAR |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR333ZAR [biosample_summary="Homo sapiens adrenal gland tissue female adult (30 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (30 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN051QBY|/analyses/ENCAN051QBY/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF765TNY|/files/ENCFF765TNY/} processed by ChIP-seq ENCODE3 hg19 pipeline has 10291068 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 {ENCFF765TNY|/files/ENCFF765TNY/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.89. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR333ZAR | float |
Histone_ChIP-seq_ENCSR333ZAR |
Histone_ChIP-seq ENCSR333ZAR [biosample_summary="Homo sapiens adrenal gland tissue female adult (30 years)" and target="H3K4me1"]
|
 |
[1.57, 11.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14588503 | 0.45% | 36814 |
| chr1 | 1518258 | 0.61% | 3697 |
| chr2 | 1224048 | 0.51% | 3147 |
| chr3 | 988650 | 0.50% | 2628 |
| chr4 | 561651 | 0.30% | 1512 |
| chr5 | 727414 | 0.40% | 1883 |
| chr6 | 733520 | 0.43% | 1971 |
| chr7 | 663009 | 0.42% | 1760 |
| chr8 | 657852 | 0.45% | 1703 |
| chr9 | 702233 | 0.51% | 1695 |
| chr10 | 759308 | 0.57% | 1912 |
| chr11 | 789828 | 0.58% | 1973 |
| chr12 | 757295 | 0.57% | 1935 |
| chr13 | 299421 | 0.26% | 806 |
| chr14 | 500595 | 0.47% | 1260 |
| chr15 | 487798 | 0.48% | 1236 |
| chr16 | 518256 | 0.57% | 1202 |
| chr17 | 763953 | 0.92% | 1789 |
| chr18 | 301007 | 0.37% | 814 |
| chr19 | 543185 | 0.93% | 1225 |
| chr20 | 451315 | 0.70% | 1087 |
| chr21 | 140787 | 0.30% | 367 |
| chr22 | 395388 | 0.78% | 890 |
| chrX | 103732 | 0.07% | 322 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 36814 | 180 | 2636 | 396.28 | 345 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF190LIL.bed.gz | 713.4 KB | ba83362cda2e3e718655f4027a891605 |
| ENCFF190LIL.tabix.bed.gz | 361.39 KB | fca7b4345df269dcd5ae9c2d6a1b5217 |
| ENCFF190LIL.tabix.bed.gz.tbi | 190.51 KB | 2ea4a6ccad9bb031222abee190edd559 |
| genomic_resource.yaml | 2.63 KB | b6f6626a0e93a30137eff81d98d9a8d8 |
| statistics/ |