Resource
| Id | Histone_ChIP-seq/ENCSR000EXB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000EXB [biosample_summary="Homo sapiens NT2/D1" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN882RJZ|/analyses/ENCAN882RJZ/} has in progress subobject document {daed34f1-b9fe-4e74-b0c4-0344ca9caa22|/documents/daed34f1-b9fe-4e74-b0c4-0344ca9caa22/} audit_internal_action: Released analysis {ENCAN882RJZ|/analyses/ENCAN882RJZ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF138NTQ|/files/ENCFF138NTQ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 13399861 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 {ENCFF623IZX|/files/ENCFF623IZX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 21107911 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 {ENCFF138NTQ|/files/ENCFF138NTQ/} 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 {ENCFF138NTQ|/files/ENCFF138NTQ/} 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_ENCSR000EXB | float |
Histone_ChIP-seq_ENCSR000EXB |
Histone_ChIP-seq ENCSR000EXB [biosample_summary="Homo sapiens NT2/D1" and target="H3K36me3"]
|
 |
[1.65, 31.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 166887053 | 5.19% | 185016 |
| chr1 | 19064872 | 7.66% | 18343 |
| chr2 | 12237759 | 5.05% | 14654 |
| chr3 | 11340555 | 5.72% | 12136 |
| chr4 | 5726095 | 3.01% | 7476 |
| chr5 | 7086716 | 3.90% | 8967 |
| chr6 | 5948015 | 3.48% | 7712 |
| chr7 | 7474594 | 4.69% | 9117 |
| chr8 | 5744705 | 3.96% | 6782 |
| chr9 | 8511206 | 6.15% | 8606 |
| chr10 | 6187281 | 4.62% | 7984 |
| chr11 | 8275844 | 6.13% | 8755 |
| chr12 | 10705527 | 8.03% | 10441 |
| chr13 | 2460784 | 2.15% | 3353 |
| chr14 | 4546780 | 4.25% | 5904 |
| chr15 | 5788709 | 5.68% | 6670 |
| chr16 | 8369164 | 9.26% | 7785 |
| chr17 | 9383688 | 11.27% | 10046 |
| chr18 | 2318212 | 2.88% | 3275 |
| chr19 | 9812909 | 16.74% | 9879 |
| chr20 | 5209307 | 8.08% | 5082 |
| chr21 | 2581440 | 5.53% | 2294 |
| chr22 | 3861964 | 7.60% | 4319 |
| chrX | 4213218 | 2.70% | 5360 |
| chrY | 37709 | 0.07% | 76 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 185016 | 158 | 39039 | 902.01 | 583 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF243SKO.bed.gz | 3.78 MB | 9e670231787695c0f0021ab6aa30d41d |
| ENCFF243SKO.tabix.bed.gz | 1.78 MB | 573f2dcc7b31a09dd6308c7b42a44846 |
| ENCFF243SKO.tabix.bed.gz.tbi | 182.77 KB | d148d2332c085681a3ea978d124a461a |
| genomic_resource.yaml | 3.93 KB | 94707d3830136e5f4c47c1802a89565e |
| statistics/ |