Resource
| Id | Histone_ChIP-seq/ENCSR000EXE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000EXE [biosample_summary="Homo sapiens NT2/D1" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN618BKQ|/analyses/ENCAN618BKQ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF193LZP|/files/ENCFF193LZP/} processed by ChIP-seq ENCODE3 hg19 pipeline has 16524523 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 {ENCFF750NEG|/files/ENCFF750NEG/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14866935 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 {ENCFF193LZP|/files/ENCFF193LZP/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF193LZP|/files/ENCFF193LZP/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.22. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000EXE | float |
Histone_ChIP-seq_ENCSR000EXE |
Histone_ChIP-seq ENCSR000EXE [biosample_summary="Homo sapiens NT2/D1" and target="H3K27me3"]
|
 |
[1.6, 56.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 47780357 | 1.49% | 43124 |
| chr1 | 4621783 | 1.86% | 4254 |
| chr2 | 3591818 | 1.48% | 3023 |
| chr3 | 2226377 | 1.12% | 2042 |
| chr4 | 1855946 | 0.98% | 1575 |
| chr5 | 2096640 | 1.15% | 1735 |
| chr6 | 2129792 | 1.25% | 1749 |
| chr7 | 2388382 | 1.50% | 2058 |
| chr8 | 2219850 | 1.53% | 2038 |
| chr9 | 2041089 | 1.47% | 1788 |
| chr10 | 2228206 | 1.67% | 2001 |
| chr11 | 2682735 | 1.99% | 2593 |
| chr12 | 2676914 | 2.01% | 2190 |
| chr13 | 874804 | 0.76% | 727 |
| chr14 | 1298724 | 1.21% | 1172 |
| chr15 | 1750302 | 1.72% | 1594 |
| chr16 | 1955106 | 2.16% | 2066 |
| chr17 | 2544002 | 3.06% | 2425 |
| chr18 | 893608 | 1.11% | 757 |
| chr19 | 2155232 | 3.68% | 2311 |
| chr20 | 2379914 | 3.69% | 2097 |
| chr21 | 536864 | 1.15% | 594 |
| chr22 | 1655713 | 3.26% | 1331 |
| chrM | 326 | 1.97% | 1 |
| chrX | 955907 | 0.61% | 964 |
| chrY | 20323 | 0.04% | 39 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 43124 | 170 | 55724 | 1107.98 | 587 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF355TTQ.bed.gz | 973.65 KB | dabd0e7a0c848817b9e3d4ace613e7ec |
| ENCFF355TTQ.tabix.bed.gz | 451.36 KB | 33afce52924be4908262d12e34666deb |
| ENCFF355TTQ.tabix.bed.gz.tbi | 132.23 KB | 786c5dee632c1a8cbb024c8d1297ef98 |
| genomic_resource.yaml | 3.67 KB | 7b55ae200c239e111f520528c8659e32 |
| statistics/ |