Resource
| Id | Histone_ChIP-seq/ENCSR997YTW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR997YTW [biosample_summary="Homo sapiens brain tissue female embryo (17 weeks)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (17 weeks) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN966ZBX|/analyses/ENCAN966ZBX/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF767NUG|/files/ENCFF767NUG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 20168275 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: Processed redacted alignments file {ENCFF017NML|/files/ENCFF017NML/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 36064234 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 {ENCFF767NUG|/files/ENCFF767NUG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF767NUG|/files/ENCFF767NUG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.20. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR997YTW | float |
Histone_ChIP-seq_ENCSR997YTW |
Histone_ChIP-seq ENCSR997YTW [biosample_summary="Homo sapiens brain tissue female embryo (17 weeks)" and target="H3K27me3"]
|
 |
[1.65, 16.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 67808732 | 2.11% | 86706 |
| chr1 | 5673858 | 2.28% | 6954 |
| chr1_KI270712v1_random | 1242 | 0.71% | 4 |
| chr1_KI270713v1_random | 7341 | 18.02% | 5 |
| chr1_KI270714v1_random | 548 | 1.31% | 2 |
| chr2 | 3769316 | 1.56% | 4329 |
| chr3 | 2154130 | 1.09% | 2901 |
| chr4 | 1924935 | 1.01% | 2055 |
| chr5 | 3493340 | 1.92% | 3981 |
| chr6 | 3597094 | 2.11% | 3990 |
| chr7 | 2507097 | 1.57% | 2722 |
| chr8 | 1874570 | 1.29% | 2094 |
| chr9 | 2387519 | 1.73% | 2687 |
| chr9_KI270718v1_random | 521 | 1.37% | 1 |
| chr10 | 3576899 | 2.67% | 4059 |
| chr11 | 2854489 | 2.11% | 3511 |
| chr12 | 3441645 | 2.58% | 4295 |
| chr13 | 996696 | 0.87% | 1126 |
| chr14 | 1839952 | 1.72% | 2104 |
| chr15 | 1877450 | 1.84% | 2310 |
| chr16 | 3294298 | 3.65% | 4225 |
| chr17 | 4246666 | 5.10% | 4595 |
| chr17_GL000205v2_random | 6706 | 3.61% | 10 |
| chr18 | 998666 | 1.24% | 1226 |
| chr19 | 4415923 | 7.53% | 5172 |
| chr20 | 2878710 | 4.47% | 3824 |
| chr21 | 603992 | 1.29% | 704 |
| chr22 | 1132228 | 2.23% | 1495 |
| chr22_KI270733v1_random | 1486 | 0.83% | 4 |
| chrUn_GL000195v1 | 333 | 0.18% | 1 |
| chrUn_KI270744v1 | 823 | 0.49% | 2 |
| chrUn_KI270754v1 | 617 | 1.54% | 2 |
| chrX | 8249642 | 5.29% | 16316 |
| 3334 contigs with no values (185251019 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 86706 | 190 | 85547 | 782.05 | 430 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF964CFA.bed.gz | 1.52 MB | efa0367b7849cd31c295cfd0a24e2cab |
| ENCFF964CFA.tabix.bed.gz | 818.35 KB | ab7a5e16ce2421ebc0c95ddb8a580b2c |
| ENCFF964CFA.tabix.bed.gz.tbi | 179.94 KB | c287ad76ffe1a45507b72737659dbb26 |
| genomic_resource.yaml | 3.75 KB | e783ba7c629d3897be4588838f7d247f |
| statistics/ |