Resource
| Id | Histone_ChIP-seq/ENCSR262VXI |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR262VXI [biosample_summary="Homo sapiens mesenchymal stem cell female adult and female adult (59 years), originated from adipose tissue" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female adult (59 years) female adult output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN711WNQ|/analyses/ENCAN711WNQ/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF071TXV|/files/ENCFF071TXV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 24934250 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 redacted alignments file {ENCFF097OLC|/files/ENCFF097OLC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 23602327 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 {ENCFF097OLC|/files/ENCFF097OLC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.80. 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 {ENCFF097OLC|/files/ENCFF097OLC/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 4.96. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR262VXI | float |
Histone_ChIP-seq_ENCSR262VXI |
Histone_ChIP-seq ENCSR262VXI [biosample_summary="Homo sapiens mesenchymal stem cell female adult and female adult (59 years), originated from adipose tissue" and target="H3K27me3"]
|
 |
[1.71, 16.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 145571882 | 4.52% | 171427 |
| chr1 | 14331322 | 5.76% | 15618 |
| chr1_KI270713v1_random | 3728 | 9.15% | 7 |
| chr2 | 9946603 | 4.11% | 11741 |
| chr3 | 7120466 | 3.59% | 8454 |
| chr4 | 4105999 | 2.16% | 4984 |
| chr5 | 6708807 | 3.70% | 7628 |
| chr6 | 5800477 | 3.40% | 6756 |
| chr7 | 5243369 | 3.29% | 6430 |
| chr8 | 5452332 | 3.76% | 6815 |
| chr9 | 6195470 | 4.48% | 7022 |
| chr10 | 7659259 | 5.72% | 8770 |
| chr11 | 9225700 | 6.83% | 10013 |
| chr12 | 6149557 | 4.61% | 6968 |
| chr13 | 2683771 | 2.35% | 3212 |
| chr14 | 4398779 | 4.11% | 5246 |
| chr15 | 5348140 | 5.24% | 5886 |
| chr16 | 4903818 | 5.43% | 5916 |
| chr17 | 8197652 | 9.85% | 8920 |
| chr17_GL000205v2_random | 36748 | 19.80% | 28 |
| chr18 | 2407148 | 2.99% | 3059 |
| chr19 | 4460765 | 7.61% | 5694 |
| chr20 | 7183452 | 11.15% | 7765 |
| chr21 | 1826498 | 3.91% | 1920 |
| chr22 | 4218263 | 8.30% | 4489 |
| chr22_KI270733v1_random | 4846 | 2.70% | 9 |
| chrUn_GL000219v1 | 10689 | 5.96% | 10 |
| chrX | 11948224 | 7.66% | 18067 |
| 3339 contigs with no values (185719194 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 171427 | 185 | 31216 | 849.18 | 578 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF541LUL.bed.gz | 3.3 MB | 282c9462d6000938fbc38f2f783297fb |
| ENCFF541LUL.tabix.bed.gz | 1.62 MB | 5e348a0b4ab82559b103222a705553b1 |
| ENCFF541LUL.tabix.bed.gz.tbi | 233.57 KB | f7ed3e23b8ee5b501cb78342a0e1ddf0 |
| genomic_resource.yaml | 4.02 KB | 743f7b83bb90be0b30efc03d99d6163c |
| statistics/ |