Resource
| Id | Histone_ChIP-seq/ENCSR143RMH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR143RMH [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (5 days) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN177FCB|/analyses/ENCAN177FCB/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN177FCB|/analyses/ENCAN177FCB/} has in progress subobject document {0752a293-f964-495b-8021-587be3b1620b|/documents/0752a293-f964-495b-8021-587be3b1620b/} audit_warning: Processed alignments file {ENCFF418YDM|/files/ENCFF418YDM/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 38773345 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 {ENCFF198YOB|/files/ENCFF198YOB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF198YOB|/files/ENCFF198YOB/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.23. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR143RMH | float |
Histone_ChIP-seq_ENCSR143RMH |
Histone_ChIP-seq ENCSR143RMH [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H3K27me3"]
|
 |
[1.61, 14.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 69194076 | 2.15% | 57740 |
| chr1 | 6823343 | 2.74% | 5608 |
| chr2 | 5663060 | 2.34% | 4747 |
| chr3 | 3755802 | 1.89% | 3344 |
| chr4 | 2909237 | 1.53% | 2406 |
| chr5 | 3497904 | 1.93% | 2939 |
| chr6 | 4294227 | 2.51% | 3372 |
| chr7 | 3518955 | 2.21% | 2984 |
| chr8 | 2893611 | 1.99% | 2639 |
| chr9 | 3051855 | 2.21% | 2573 |
| chr10 | 4283198 | 3.20% | 3640 |
| chr11 | 4232950 | 3.13% | 3711 |
| chr12 | 3593053 | 2.70% | 2677 |
| chr13 | 2021187 | 1.77% | 1591 |
| chr14 | 2135917 | 2.00% | 1682 |
| chr15 | 2587160 | 2.54% | 2087 |
| chr16 | 2549771 | 2.82% | 2363 |
| chr17 | 2967067 | 3.56% | 2388 |
| chr18 | 1763771 | 2.19% | 1463 |
| chr19 | 1473277 | 2.51% | 1136 |
| chr20 | 2411864 | 3.74% | 2127 |
| chr21 | 448715 | 0.96% | 365 |
| chr22 | 1660824 | 3.27% | 1387 |
| chrX | 657328 | 0.42% | 511 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 57740 | 205 | 90974 | 1198.37 | 705 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF817CHW.bed.gz | 1.14 MB | c6f3d360dac1fea0b8000155fd786a00 |
| ENCFF817CHW.tabix.bed.gz | 580.93 KB | 82e7bd9dc35e5f1608bb65d57a7e88c4 |
| ENCFF817CHW.tabix.bed.gz.tbi | 170.17 KB | ce01719cf8d25f1c4d151f8370a96e7e |
| genomic_resource.yaml | 3.48 KB | a805a571bfab2082e533d946690c078a |
| statistics/ |