Resource
| Id | Histone_ChIP-seq/ENCSR199VMI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR199VMI [biosample_summary="Homo sapiens subcutaneous abdominal adipose tissue tissue nuclear fraction female adult (25 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (25 years) nuclear fraction output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN476ATK|/analyses/ENCAN476ATK/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF699TVR|/files/ENCFF699TVR/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 29185001 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 {ENCFF699TVR|/files/ENCFF699TVR/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF699TVR|/files/ENCFF699TVR/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.33. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR199VMI | float |
Histone_ChIP-seq_ENCSR199VMI |
Histone_ChIP-seq ENCSR199VMI [biosample_summary="Homo sapiens subcutaneous abdominal adipose tissue tissue nuclear fraction female adult (25 years)" and target="H3K4me1"]
|
 |
[1.62, 34.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 150289265 | 4.67% | 163010 |
| chr1 | 14218217 | 5.71% | 15030 |
| chr2 | 12245893 | 5.06% | 13522 |
| chr3 | 10227357 | 5.16% | 11263 |
| chr4 | 5688836 | 2.99% | 6923 |
| chr5 | 8207649 | 4.52% | 9111 |
| chr6 | 8125212 | 4.76% | 9467 |
| chr7 | 7522481 | 4.72% | 8529 |
| chr8 | 6543213 | 4.51% | 7471 |
| chr9 | 6918847 | 5.00% | 7232 |
| chr10 | 8099269 | 6.05% | 8591 |
| chr11 | 8544406 | 6.33% | 8639 |
| chr12 | 7235647 | 5.43% | 7885 |
| chr13 | 3498766 | 3.06% | 4047 |
| chr14 | 4957973 | 4.63% | 5156 |
| chr15 | 5188305 | 5.09% | 5367 |
| chr16 | 5171834 | 5.72% | 5264 |
| chr17 | 7553145 | 9.07% | 7370 |
| chr18 | 3030800 | 3.77% | 3485 |
| chr19 | 5345530 | 9.12% | 5367 |
| chr20 | 4310910 | 6.69% | 4488 |
| chr21 | 1750098 | 3.75% | 1967 |
| chr22 | 3510002 | 6.91% | 3414 |
| chrX | 2394875 | 1.53% | 3422 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 163010 | 175 | 28379 | 921.96 | 692 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF397JTT.bed.gz | 3.5 MB | b06bc5fb15f8a8477e353cf62d68949f |
| ENCFF397JTT.tabix.bed.gz | 1.63 MB | 70de00f8f6681575220d94a144bebe71 |
| ENCFF397JTT.tabix.bed.gz.tbi | 390.56 KB | 54c15327e98f65ab7ff91a060c13f025 |
| genomic_resource.yaml | 3.46 KB | e6494e971086ed82d623c897abffee1f |
| statistics/ |