Resource
| Id | Histone_ChIP-seq/ENCSR000DST |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DST [biosample_summary="Homo sapiens H7" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN621OIG|/analyses/ENCAN621OIG/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN621OIG|/analyses/ENCAN621OIG/} has in progress subobject document {d3ae894c-bb95-4fba-a1d2-afc550e8f507|/documents/d3ae894c-bb95-4fba-a1d2-afc550e8f507/} audit_not_compliant: Processed alignments file {ENCFF198VKK|/files/ENCFF198VKK/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 9837107 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 {ENCFF250SOU|/files/ENCFF250SOU/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline has 16969020 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 {ENCFF250SOU|/files/ENCFF250SOU/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF250SOU|/files/ENCFF250SOU/} processed by ChIP-seq ENCODE4 v1.6.0 GRCh38 pipeline was generated from a library with PBC2 value of 9.91. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DST | float |
Histone_ChIP-seq_ENCSR000DST |
Histone_ChIP-seq ENCSR000DST [biosample_summary="Homo sapiens H7" and target="H3K27me3"]
|
 |
[1.96, 57.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 32232897 | 1.00% | 44860 |
| chr1 | 3549519 | 1.43% | 5656 |
| chr2 | 2306454 | 0.95% | 3006 |
| chr3 | 1363583 | 0.69% | 2103 |
| chr4 | 1440043 | 0.76% | 1746 |
| chr5 | 1685343 | 0.93% | 2154 |
| chr6 | 1970994 | 1.15% | 2524 |
| chr7 | 1630955 | 1.02% | 1989 |
| chr8 | 1326427 | 0.91% | 1808 |
| chr9 | 1386515 | 1.00% | 2070 |
| chr10 | 1677642 | 1.25% | 2029 |
| chr11 | 1674999 | 1.24% | 2527 |
| chr12 | 1722781 | 1.29% | 2257 |
| chr13 | 727594 | 0.64% | 966 |
| chr14 | 968611 | 0.90% | 1306 |
| chr15 | 1058808 | 1.04% | 1428 |
| chr16 | 971357 | 1.08% | 1406 |
| chr17 | 1804327 | 2.17% | 2351 |
| chr18 | 649201 | 0.81% | 943 |
| chr19 | 1340909 | 2.29% | 2225 |
| chr20 | 882243 | 1.37% | 1332 |
| chr21 | 253810 | 0.54% | 343 |
| chr22 | 916238 | 1.80% | 1288 |
| chrX | 924544 | 0.59% | 1403 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44860 | 135 | 61905 | 718.52 | 316 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF662NTZ.bed.gz | 865.23 KB | 1e5f5edb6be222d62d4b2148487ab7ef |
| ENCFF662NTZ.tabix.bed.gz | 438.89 KB | 74f9743772497634163344a97ff121cf |
| ENCFF662NTZ.tabix.bed.gz.tbi | 120.06 KB | 8c3a59fdae92c5c39ea97d252e5d405d |
| genomic_resource.yaml | 4.22 KB | f3dad0fd5a95ea01aec4d3b383b331a2 |
| statistics/ |