Resource
| Id | Histone_ChIP-seq/ENCSR393HDC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR393HDC [biosample_summary="Homo sapiens neurosphere female embryo (17 weeks) originated from cortex" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (17 weeks) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN848YNB|/analyses/ENCAN848YNB/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} 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 {ENCFF838ILC|/files/ENCFF838ILC/} 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 redacted alignments file {ENCFF838ILC|/files/ENCFF838ILC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.91. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR393HDC | float |
Histone_ChIP-seq_ENCSR393HDC |
Histone_ChIP-seq ENCSR393HDC [biosample_summary="Homo sapiens neurosphere female embryo (17 weeks) originated from cortex" and target="H3K9me3"]
|
 |
[1.83, 24.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 70492173 | 2.19% | 133449 |
| chr1 | 4316299 | 1.73% | 8728 |
| chr2 | 4627689 | 1.91% | 9547 |
| chr3 | 3662902 | 1.85% | 7738 |
| chr4 | 3588984 | 1.89% | 7105 |
| chr5 | 4032117 | 2.22% | 7713 |
| chr6 | 3132858 | 1.83% | 6700 |
| chr7 | 4949881 | 3.11% | 8490 |
| chr8 | 3656871 | 2.52% | 6547 |
| chr9 | 2399168 | 1.73% | 4756 |
| chr10 | 2913013 | 2.18% | 5480 |
| chr11 | 3210312 | 2.38% | 6032 |
| chr12 | 3238238 | 2.43% | 5729 |
| chr13 | 1879570 | 1.64% | 3820 |
| chr14 | 2154700 | 2.01% | 4317 |
| chr15 | 2055744 | 2.02% | 3940 |
| chr16 | 2257179 | 2.50% | 3928 |
| chr17 | 1551263 | 1.86% | 2966 |
| chr18 | 1366338 | 1.70% | 2889 |
| chr19 | 5556456 | 9.48% | 6809 |
| chr20 | 1247679 | 1.94% | 2471 |
| chr21 | 1303488 | 2.79% | 2255 |
| chr22 | 786779 | 1.55% | 1493 |
| chrM | 12204 | 73.66% | 12 |
| chrX | 6461090 | 4.14% | 13664 |
| chrY | 131351 | 0.23% | 320 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 133449 | 105 | 46679 | 528.23 | 375 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF928XVT.bed.gz | 2.41 MB | fc25772b596981a7ccf9454b6c23a9a4 |
| ENCFF928XVT.tabix.bed.gz | 1.23 MB | 3fcb0b1a48f8dff2cb9ec92da78a2f6a |
| ENCFF928XVT.tabix.bed.gz.tbi | 415.35 KB | 3f7fa18b41138d6236c19c3c7b6b27e1 |
| genomic_resource.yaml | 2.84 KB | e8845252ceba3614a7f78e4499294c3f |
| statistics/ |