Resource
| Id | Histone_ChIP-seq/ENCSR203RKZ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR203RKZ [biosample_summary="Homo sapiens liver tissue male adult (78 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (78 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN917IQU|/analyses/ENCAN917IQU/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF952GVO|/files/ENCFF952GVO/} processed by ChIP-seq ENCODE3 hg19 pipeline has 17021472 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 redacted alignments file {ENCFF952GVO|/files/ENCFF952GVO/} 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 redacted alignments file {ENCFF952GVO|/files/ENCFF952GVO/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.26. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR203RKZ | float |
Histone_ChIP-seq_ENCSR203RKZ |
Histone_ChIP-seq ENCSR203RKZ [biosample_summary="Homo sapiens liver tissue male adult (78 years)" and target="H3K4me1"]
|
 |
[1.38, 30.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 83691970 | 2.60% | 113273 |
| chr1 | 8220456 | 3.30% | 11078 |
| chr2 | 6218623 | 2.57% | 8604 |
| chr3 | 5379958 | 2.71% | 7342 |
| chr4 | 3244522 | 1.71% | 4780 |
| chr5 | 4072886 | 2.24% | 5623 |
| chr6 | 4311752 | 2.52% | 6200 |
| chr7 | 3844539 | 2.41% | 5481 |
| chr8 | 3413946 | 2.35% | 4764 |
| chr9 | 4099403 | 2.96% | 5181 |
| chr10 | 4110225 | 3.07% | 5689 |
| chr11 | 4789616 | 3.55% | 6151 |
| chr12 | 4144202 | 3.11% | 5767 |
| chr13 | 1771822 | 1.55% | 2620 |
| chr14 | 2746155 | 2.57% | 3591 |
| chr15 | 2903620 | 2.85% | 3975 |
| chr16 | 3491990 | 3.87% | 4388 |
| chr17 | 4482303 | 5.38% | 5581 |
| chr18 | 1606276 | 2.00% | 2328 |
| chr19 | 3535356 | 6.03% | 4405 |
| chr20 | 2500342 | 3.88% | 3281 |
| chr21 | 917271 | 1.96% | 1227 |
| chr22 | 2353062 | 4.63% | 2824 |
| chrM | 2371 | 14.31% | 3 |
| chrX | 1531274 | 0.98% | 2390 |
| 3342 contigs with no values (186287931 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 113273 | 170 | 39954 | 738.85 | 561 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF713BKS.bed.gz | 2.37 MB | d3db32dcd34d69878a2a5aeb87751fab |
| ENCFF713BKS.tabix.bed.gz | 1.12 MB | ad58e027ce38918faebdede4adf045f7 |
| ENCFF713BKS.tabix.bed.gz.tbi | 298.77 KB | 8cef20cf6e0800f428714e6c62ac2c12 |
| genomic_resource.yaml | 3.24 KB | b8b866cd209c32a6182d29748cbb288c |
| statistics/ |