Resource
| Id | Histone_ChIP-seq/ENCSR301HRV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR301HRV [biosample_summary="Homo sapiens H1" and target="H3K79me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN381NBA|/analyses/ENCAN381NBA/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN381NBA|/analyses/ENCAN381NBA/} has in progress subobject document {2fbea9e2-f574-4487-b998-6614855125eb|/documents/2fbea9e2-f574-4487-b998-6614855125eb/} audit_not_compliant: Processed alignments file {ENCFF499XCE|/files/ENCFF499XCE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 14543920 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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_not_compliant: Processed alignments file {ENCFF015TSL|/files/ENCFF015TSL/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 25772374 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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 {ENCFF015TSL|/files/ENCFF015TSL/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF015TSL|/files/ENCFF015TSL/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.84. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR301HRV | float |
Histone_ChIP-seq_ENCSR301HRV |
Histone_ChIP-seq ENCSR301HRV [biosample_summary="Homo sapiens H1" and target="H3K79me2"]
|
 |
[1.68, 15.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 14244463 | 0.44% | 22414 |
| chr1 | 1437528 | 0.58% | 2226 |
| chr2 | 1099069 | 0.45% | 1835 |
| chr3 | 888466 | 0.45% | 1399 |
| chr4 | 589838 | 0.31% | 954 |
| chr5 | 829225 | 0.46% | 1234 |
| chr6 | 875737 | 0.51% | 1306 |
| chr7 | 742330 | 0.47% | 1223 |
| chr8 | 610183 | 0.42% | 1009 |
| chr9 | 515866 | 0.37% | 854 |
| chr10 | 611307 | 0.46% | 962 |
| chr11 | 612032 | 0.45% | 977 |
| chr12 | 663577 | 0.50% | 1056 |
| chr13 | 298505 | 0.26% | 532 |
| chr14 | 424242 | 0.40% | 730 |
| chr15 | 415195 | 0.41% | 731 |
| chr16 | 558173 | 0.62% | 837 |
| chr17 | 716910 | 0.86% | 1039 |
| chr18 | 265135 | 0.33% | 469 |
| chr19 | 755557 | 1.29% | 993 |
| chr20 | 508683 | 0.79% | 709 |
| chr21 | 204497 | 0.44% | 326 |
| chr22 | 426673 | 0.84% | 677 |
| chrX | 184244 | 0.12% | 311 |
| chrY | 11491 | 0.02% | 25 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 22414 | 238 | 12019 | 635.52 | 458 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF620GIW.bed.gz | 464.06 KB | fcabb67cb4ed1b188045a191889fdfe9 |
| ENCFF620GIW.tabix.bed.gz | 232.14 KB | 5af4cd4543c975aec6f46aae69fb43f9 |
| ENCFF620GIW.tabix.bed.gz.tbi | 75.28 KB | 9c50c4799e0b5f3240ea2dcf1c600099 |
| genomic_resource.yaml | 3.92 KB | 8b8dcca1053554035f7bede1705c2ace |
| statistics/ |