Resource
| Id | Histone_ChIP-seq/ENCSR262NQD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR262NQD [biosample_summary="Homo sapiens HUES48" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN941CWV|/analyses/ENCAN941CWV/} has in progress subobject document {05be471d-c840-481c-bc71-047b0de47cda|/documents/05be471d-c840-481c-bc71-047b0de47cda/} audit_internal_action: Released analysis {ENCAN941CWV|/analyses/ENCAN941CWV/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF907NYZ|/files/ENCFF907NYZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 18855229 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 {ENCFF774DQE|/files/ENCFF774DQE/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 21248859 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 {ENCFF907NYZ|/files/ENCFF907NYZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 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 {ENCFF907NYZ|/files/ENCFF907NYZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.15. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR262NQD | float |
Histone_ChIP-seq_ENCSR262NQD |
Histone_ChIP-seq ENCSR262NQD [biosample_summary="Homo sapiens HUES48" and target="H3K27me3"]
|
 |
[1.81, 61.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 52046446 | 1.62% | 36708 |
| chr1 | 4977136 | 2.00% | 3558 |
| chr2 | 3870676 | 1.60% | 2607 |
| chr3 | 2421593 | 1.22% | 1685 |
| chr4 | 2316621 | 1.22% | 1369 |
| chr5 | 2741963 | 1.51% | 1775 |
| chr6 | 2972012 | 1.74% | 1773 |
| chr7 | 2499266 | 1.57% | 1576 |
| chr8 | 2205198 | 1.52% | 1434 |
| chr9 | 2396005 | 1.73% | 1817 |
| chr10 | 2659798 | 1.99% | 1638 |
| chr11 | 2944114 | 2.18% | 2151 |
| chr12 | 2783506 | 2.09% | 1869 |
| chr13 | 1246719 | 1.09% | 826 |
| chr14 | 1613626 | 1.51% | 1077 |
| chr15 | 1649597 | 1.62% | 1120 |
| chr16 | 1442350 | 1.60% | 1052 |
| chr17 | 2616831 | 3.14% | 1763 |
| chr18 | 1081950 | 1.35% | 729 |
| chr19 | 1573235 | 2.68% | 1310 |
| chr20 | 1527712 | 2.37% | 1199 |
| chr21 | 437923 | 0.94% | 328 |
| chr22 | 1485447 | 2.92% | 1035 |
| chrX | 2583168 | 1.66% | 3017 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 36708 | 173 | 112059 | 1417.85 | 724 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF612HRW.bed.gz | 871.23 KB | 41ef991b8042c7b54d6f61ff6a4486d8 |
| ENCFF612HRW.tabix.bed.gz | 395.29 KB | dd2b327528ada767a1fa069a51f10951 |
| ENCFF612HRW.tabix.bed.gz.tbi | 127.14 KB | bb29c934d843c8584de998a417ca6eb0 |
| genomic_resource.yaml | 3.93 KB | b78ebfa582ba9d8015234bca9fe6671c |
| statistics/ |