Resource
| Id | Histone_ChIP-seq/ENCSR770GNM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR770GNM [biosample_summary="Homo sapiens mucosa of stomach tissue male adult (59 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (59 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN956SUH|/analyses/ENCAN956SUH/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF416QJY|/files/ENCFF416QJY/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 29859835 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 redacted alignments file {ENCFF416QJY|/files/ENCFF416QJY/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.79. 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 redacted alignments file {ENCFF416QJY|/files/ENCFF416QJY/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 4.62. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR770GNM | float |
Histone_ChIP-seq_ENCSR770GNM |
Histone_ChIP-seq ENCSR770GNM [biosample_summary="Homo sapiens mucosa of stomach tissue male adult (59 years)" and target="H3K27me3"]
|
 |
[1.79, 22.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 35649567 | 1.11% | 40093 |
| chr1 | 3676534 | 1.48% | 4233 |
| chr2 | 2539492 | 1.05% | 2732 |
| chr3 | 1559767 | 0.79% | 1853 |
| chr4 | 1313264 | 0.69% | 1269 |
| chr5 | 1917974 | 1.06% | 2015 |
| chr6 | 2112198 | 1.24% | 2257 |
| chr7 | 1844873 | 1.16% | 1973 |
| chr8 | 1414115 | 0.97% | 1641 |
| chr9 | 1608047 | 1.16% | 1806 |
| chr10 | 1991279 | 1.49% | 2194 |
| chr11 | 1968722 | 1.46% | 2234 |
| chr12 | 1815753 | 1.36% | 1986 |
| chr13 | 765406 | 0.67% | 847 |
| chr14 | 1119323 | 1.05% | 1321 |
| chr15 | 1151507 | 1.13% | 1341 |
| chr16 | 1196372 | 1.32% | 1461 |
| chr17 | 2567786 | 3.08% | 2833 |
| chr18 | 544432 | 0.68% | 678 |
| chr19 | 1673149 | 2.85% | 1900 |
| chr20 | 1341292 | 2.08% | 1558 |
| chr21 | 358093 | 0.77% | 447 |
| chr22 | 841419 | 1.66% | 1110 |
| chrX | 325403 | 0.21% | 399 |
| chrY | 3367 | 0.01% | 5 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40093 | 220 | 26447 | 889.17 | 563 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF299KZS.bed.gz | 778.44 KB | 307d4bcbaf97f127ce005a5f3982818b |
| ENCFF299KZS.tabix.bed.gz | 394.18 KB | 1a55ed0c4167519a44a5985d5b49a673 |
| ENCFF299KZS.tabix.bed.gz.tbi | 137.08 KB | c51b6bf3022c8edd6d31daf52c41ce23 |
| genomic_resource.yaml | 3.3 KB | c101f713b673f934984b0953cf2fc827 |
| statistics/ |