Resource
| Id | Histone_ChIP-seq/ENCSR438ZIS |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR438ZIS [biosample_summary="Homo sapiens neurosphere female embryo (17 weeks) originated from cortex" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (17 weeks) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN065FIP|/analyses/ENCAN065FIP/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF695ZXU|/files/ENCFF695ZXU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 27101619 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 {ENCFF695ZXU|/files/ENCFF695ZXU/} processed by ChIP-seq ENCODE3 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 redacted alignments file {ENCFF695ZXU|/files/ENCFF695ZXU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.79. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR438ZIS | float |
Histone_ChIP-seq_ENCSR438ZIS |
Histone_ChIP-seq ENCSR438ZIS [biosample_summary="Homo sapiens neurosphere female embryo (17 weeks) originated from cortex" and target="H3K27me3"]
|
 |
[1.61, 24.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 60893503 | 1.89% | 69239 |
| chr1 | 6043402 | 2.43% | 6673 |
| chr1_KI270712v1_random | 613 | 0.35% | 2 |
| chr1_KI270713v1_random | 7830 | 19.22% | 7 |
| chr2 | 3797576 | 1.57% | 4395 |
| chr3 | 3170121 | 1.60% | 3824 |
| chr4 | 2382492 | 1.25% | 2420 |
| chr5 | 3086818 | 1.70% | 3240 |
| chr6 | 3327740 | 1.95% | 3525 |
| chr7 | 3042708 | 1.91% | 3164 |
| chr8 | 2086817 | 1.44% | 2305 |
| chr9 | 2646233 | 1.91% | 3035 |
| chr10 | 3478096 | 2.60% | 3772 |
| chr11 | 4035793 | 2.99% | 4514 |
| chr12 | 2504025 | 1.88% | 2730 |
| chr13 | 1042047 | 0.91% | 1223 |
| chr14 | 1996045 | 1.86% | 2274 |
| chr15 | 2325826 | 2.28% | 2808 |
| chr16 | 2196416 | 2.43% | 2434 |
| chr17 | 3070069 | 3.69% | 3171 |
| chr17_GL000205v2_random | 5613 | 3.02% | 4 |
| chr18 | 1031324 | 1.28% | 1228 |
| chr19 | 1535939 | 2.62% | 1561 |
| chr20 | 3039024 | 4.72% | 3658 |
| chr21 | 513501 | 1.10% | 595 |
| chr22 | 1592836 | 3.13% | 2029 |
| chrM | 2196 | 13.25% | 4 |
| chrUn_KI270438v1 | 351 | 0.31% | 1 |
| chrX | 2932052 | 1.88% | 4643 |
| 3338 contigs with no values (185773047 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 69239 | 180 | 59837 | 879.47 | 548 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF386OXO.bed.gz | 1.31 MB | c42e8724e298fc5a9c79634e053c515a |
| ENCFF386OXO.tabix.bed.gz | 678.06 KB | 0cb259469fa2352e0c67fb77b9eef63a |
| ENCFF386OXO.tabix.bed.gz.tbi | 157.69 KB | f39356fcf56a6256ec3508858a45925b |
| genomic_resource.yaml | 3.34 KB | 684df0772dd695696c099efef867dfc9 |
| statistics/ |