Resource
| Id | Histone_ChIP-seq/ENCSR253WND |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR253WND [biosample_summary="Homo sapiens heart right ventricle tissue male adult (55 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (55 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN749BLM|/analyses/ENCAN749BLM/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_warning: Processed alignments file {ENCFF370TUZ|/files/ENCFF370TUZ/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline has 38431113 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 {ENCFF370TUZ|/files/ENCFF370TUZ/} processed by ChIP-seq ENCODE4 v1.8.0 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 alignments file {ENCFF370TUZ|/files/ENCFF370TUZ/} processed by ChIP-seq ENCODE4 v1.8.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.46. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR253WND | float |
Histone_ChIP-seq_ENCSR253WND |
Histone_ChIP-seq ENCSR253WND [biosample_summary="Homo sapiens heart right ventricle tissue male adult (55 years)" and target="H3K4me1"]
|
 |
[1.78, 20.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 186631672 | 5.80% | 155732 |
| chr1 | 18673010 | 7.50% | 15198 |
| chr2 | 15279890 | 6.31% | 12862 |
| chr3 | 13586828 | 6.85% | 11230 |
| chr4 | 8088655 | 4.25% | 7271 |
| chr5 | 10737970 | 5.91% | 9170 |
| chr6 | 10851600 | 6.35% | 9618 |
| chr7 | 8932680 | 5.61% | 7978 |
| chr8 | 8295792 | 5.72% | 7146 |
| chr9 | 7846381 | 5.67% | 6399 |
| chr10 | 10415559 | 7.78% | 8345 |
| chr11 | 9581746 | 7.09% | 7792 |
| chr12 | 9299572 | 6.98% | 7650 |
| chr13 | 4934241 | 4.31% | 4254 |
| chr14 | 6002437 | 5.61% | 4900 |
| chr15 | 6970879 | 6.83% | 5618 |
| chr16 | 5869135 | 6.50% | 4853 |
| chr17 | 8574810 | 10.30% | 6523 |
| chr18 | 4057175 | 5.05% | 3611 |
| chr19 | 5533098 | 9.44% | 4449 |
| chr20 | 4962900 | 7.70% | 3916 |
| chr21 | 1859431 | 3.98% | 1620 |
| chr22 | 4291007 | 8.44% | 3200 |
| chrX | 1921980 | 1.23% | 2050 |
| chrY | 64896 | 0.11% | 79 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 155732 | 190 | 45625 | 1198.42 | 848 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF008WTY.bed.gz | 3.48 MB | eccb354f741e1efbcb78d35c782ad87b |
| ENCFF008WTY.tabix.bed.gz | 1.59 MB | e4b8acdf38348182e684d9821e222256 |
| ENCFF008WTY.tabix.bed.gz.tbi | 328.55 KB | fd41f1d41f9ecb0ed3d68fc014081ac8 |
| genomic_resource.yaml | 3.28 KB | d838c6bd55d7513e1075b462bc721818 |
| statistics/ |