Resource
| Id | Histone_ChIP-seq/ENCSR214WRA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR214WRA [biosample_summary="Homo sapiens iPS-20b" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN701XIL|/analyses/ENCAN701XIL/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed unfiltered alignments file {ENCFF101UEL|/files/ENCFF101UEL/} processed by ChIP-seq ENCODE3 hg19 pipeline has 19045100 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed unfiltered alignments file {ENCFF097SGA|/files/ENCFF097SGA/} processed by ChIP-seq ENCODE3 hg19 pipeline has 36333931 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF333YFW|/files/ENCFF333YFW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.88. 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 {ENCFF333YFW|/files/ENCFF333YFW/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.24. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR214WRA | float |
Histone_ChIP-seq_ENCSR214WRA |
Histone_ChIP-seq ENCSR214WRA [biosample_summary="Homo sapiens iPS-20b" and target="H3K9me3"]
|
 |
[1.87, 44.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 74506120 | 2.32% | 97322 |
| chr1 | 4687093 | 1.88% | 6441 |
| chr2 | 4474101 | 1.85% | 6795 |
| chr3 | 3355404 | 1.69% | 5203 |
| chr4 | 4382197 | 2.30% | 6322 |
| chr5 | 4377014 | 2.41% | 5842 |
| chr6 | 3237607 | 1.90% | 4865 |
| chr7 | 5748210 | 3.61% | 6840 |
| chr8 | 4387556 | 3.02% | 4880 |
| chr9 | 2199163 | 1.59% | 3078 |
| chr10 | 3381083 | 2.53% | 4426 |
| chr11 | 4027086 | 2.98% | 4982 |
| chr12 | 3843257 | 2.88% | 4636 |
| chr13 | 2022135 | 1.77% | 2878 |
| chr14 | 2861771 | 2.67% | 3511 |
| chr15 | 1924161 | 1.89% | 2826 |
| chr16 | 2630100 | 2.91% | 2772 |
| chr17 | 1421273 | 1.71% | 2026 |
| chr18 | 1423321 | 1.77% | 2084 |
| chr19 | 8152270 | 13.91% | 7726 |
| chr20 | 1254452 | 1.95% | 1748 |
| chr21 | 1303804 | 2.79% | 1760 |
| chr22 | 552413 | 1.09% | 844 |
| chrX | 1927596 | 1.24% | 3409 |
| chrY | 933053 | 1.63% | 1428 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 97322 | 185 | 59246 | 765.56 | 520 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF827EDV.bed.gz | 1.78 MB | 625f6a219124c2aff167ef27819c76f3 |
| ENCFF827EDV.tabix.bed.gz | 923.98 KB | be8b47e12c05673fe540013cad873b61 |
| ENCFF827EDV.tabix.bed.gz.tbi | 309.2 KB | 2cc303a579273f1a4032e933f9866d84 |
| genomic_resource.yaml | 3.66 KB | 35c6aa9338ef4e32e7052e1fc49989a7 |
| statistics/ |