Resource
| Id | Histone_ChIP-seq/ENCSR778VGY |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR778VGY [biosample_summary="Homo sapiens ACC112" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN982KEG|/analyses/ENCAN982KEG/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF785BFN|/files/ENCFF785BFN/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 11265212 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 {ENCFF785BFN|/files/ENCFF785BFN/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF785BFN|/files/ENCFF785BFN/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.79. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR778VGY | float |
Histone_ChIP-seq_ENCSR778VGY |
Histone_ChIP-seq ENCSR778VGY [biosample_summary="Homo sapiens ACC112" and target="H3K4me3"]
|
 |
[1.49, 55.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 74439608 | 2.31% | 62339 |
| chr1 | 6984416 | 2.81% | 5682 |
| chr1_KI270712v1_random | 282 | 0.16% | 1 |
| chr1_KI270713v1_random | 220 | 0.54% | 1 |
| chr2 | 5816038 | 2.40% | 5124 |
| chr3 | 4911499 | 2.48% | 4275 |
| chr4 | 3815264 | 2.01% | 3476 |
| chr5 | 4024824 | 2.22% | 3525 |
| chr6 | 4685436 | 2.74% | 3923 |
| chr7 | 3682147 | 2.31% | 3192 |
| chr8 | 3233824 | 2.23% | 2891 |
| chr9 | 3169907 | 2.29% | 2686 |
| chr10 | 3346032 | 2.50% | 2815 |
| chr11 | 3851797 | 2.85% | 3048 |
| chr12 | 3913932 | 2.94% | 3189 |
| chr13 | 1721403 | 1.51% | 1614 |
| chr14 | 2465843 | 2.30% | 1962 |
| chr15 | 2439160 | 2.39% | 1992 |
| chr16 | 2373206 | 2.63% | 1807 |
| chr17 | 3502975 | 4.21% | 2659 |
| chr17_GL000205v2_random | 2486 | 1.34% | 2 |
| chr18 | 1584021 | 1.97% | 1471 |
| chr19 | 3021271 | 5.15% | 2174 |
| chr20 | 1644685 | 2.55% | 1356 |
| chr21 | 773419 | 1.66% | 684 |
| chr22 | 1144879 | 2.25% | 893 |
| chrUn_GL000195v1 | 292 | 0.16% | 1 |
| chrUn_GL000219v1 | 2775 | 1.55% | 3 |
| chrX | 2256721 | 1.45% | 1840 |
| chrY | 70854 | 0.12% | 53 |
| 3337 contigs with no values (128312612 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 62339 | 210 | 21493 | 1194.11 | 751 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF712OJP.bed.gz | 1.66 MB | b13a58d2950eb2e70311c57c515eac6d |
| ENCFF712OJP.tabix.bed.gz | 708.51 KB | d0676542f5033d3d3cba9e9129654626 |
| ENCFF712OJP.tabix.bed.gz.tbi | 289.76 KB | 8f27cc8ffab050c084dff8242731fdce |
| genomic_resource.yaml | 3.17 KB | c407e9948445be556c487f8ce9b5ef4b |
| statistics/ |