Resource
| Id | Histone_ChIP-seq/ENCSR835YBD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR835YBD [biosample_summary="Homo sapiens KMS-11" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN637GVQ|/analyses/ENCAN637GVQ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN637GVQ|/analyses/ENCAN637GVQ/} has in progress subobject document {93ecfd7f-a7b0-473f-962a-c04dae582175|/documents/93ecfd7f-a7b0-473f-962a-c04dae582175/} audit_not_compliant: Processed alignments file {ENCFF786COH|/files/ENCFF786COH/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 22092626 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 {ENCFF125PEN|/files/ENCFF125PEN/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 19092469 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 {ENCFF125PEN|/files/ENCFF125PEN/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF125PEN|/files/ENCFF125PEN/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.34. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR835YBD | float |
Histone_ChIP-seq_ENCSR835YBD |
Histone_ChIP-seq ENCSR835YBD [biosample_summary="Homo sapiens KMS-11" and target="H3K36me3"]
|
 |
[1.79, 6.59] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 10732425 | 0.33% | 16453 |
| chr1 | 1568820 | 0.63% | 2165 |
| chr2 | 871130 | 0.36% | 1366 |
| chr3 | 508963 | 0.26% | 749 |
| chr4 | 388658 | 0.20% | 614 |
| chr5 | 581239 | 0.32% | 935 |
| chr6 | 379574 | 0.22% | 617 |
| chr7 | 888631 | 0.56% | 1361 |
| chr8 | 456292 | 0.31% | 736 |
| chr9 | 391568 | 0.28% | 672 |
| chr10 | 518706 | 0.39% | 853 |
| chr11 | 377573 | 0.28% | 592 |
| chr12 | 626776 | 0.47% | 859 |
| chr13 | 27591 | 0.02% | 58 |
| chr14 | 68017 | 0.06% | 123 |
| chr15 | 298214 | 0.29% | 530 |
| chr16 | 562386 | 0.62% | 851 |
| chr17 | 630138 | 0.76% | 928 |
| chr18 | 319966 | 0.40% | 479 |
| chr19 | 505122 | 0.86% | 777 |
| chr20 | 388199 | 0.60% | 570 |
| chr21 | 156083 | 0.33% | 237 |
| chr22 | 167928 | 0.33% | 282 |
| chrX | 50851 | 0.03% | 99 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 16453 | 193 | 9598 | 652.31 | 528 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF935NGI.bed.gz | 358.18 KB | 7d2d8900ad6e2d9bf5f992c6684924f1 |
| ENCFF935NGI.tabix.bed.gz | 172.74 KB | 3b1247449196dc8680acb97d9abb12ea |
| ENCFF935NGI.tabix.bed.gz.tbi | 66.99 KB | 55ca7528d549a5e93d05f11d5780c30a |
| genomic_resource.yaml | 3.93 KB | eb68abf247fab458a667cefcc386d353 |
| statistics/ |