Resource
| Id | Histone_ChIP-seq/ENCSR484MFB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR484MFB [biosample_summary="Homo sapiens hepatocyte originated from H9" and target="H3K9me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (5 days) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN478EYC|/analyses/ENCAN478EYC/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF101CWO|/files/ENCFF101CWO/} processed by ChIP-seq ENCODE3 hg19 pipeline has 27674739 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me2-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 alignments file {ENCFF521JBV|/files/ENCFF521JBV/} processed by ChIP-seq ENCODE3 hg19 pipeline has 21550265 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me2-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 alignments file {ENCFF521JBV|/files/ENCFF521JBV/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.81. 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 {ENCFF521JBV|/files/ENCFF521JBV/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 5.04. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR484MFB | float |
Histone_ChIP-seq_ENCSR484MFB |
Histone_ChIP-seq ENCSR484MFB [biosample_summary="Homo sapiens hepatocyte originated from H9" and target="H3K9me2"]
|
 |
[1.46, 4.86] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 584528 | 0.02% | 1678 |
| chr1 | 44004 | 0.02% | 131 |
| chr2 | 50187 | 0.02% | 151 |
| chr3 | 43613 | 0.02% | 124 |
| chr4 | 45833 | 0.02% | 137 |
| chr5 | 40338 | 0.02% | 120 |
| chr6 | 37456 | 0.02% | 102 |
| chr7 | 33460 | 0.02% | 100 |
| chr8 | 27928 | 0.02% | 79 |
| chr9 | 16861 | 0.01% | 53 |
| chr10 | 25098 | 0.02% | 70 |
| chr11 | 20870 | 0.02% | 62 |
| chr12 | 21117 | 0.02% | 66 |
| chr13 | 23767 | 0.02% | 71 |
| chr14 | 17226 | 0.02% | 49 |
| chr15 | 12233 | 0.01% | 36 |
| chr16 | 15296 | 0.02% | 43 |
| chr17 | 7017 | 0.01% | 21 |
| chr18 | 22059 | 0.03% | 63 |
| chr19 | 7556 | 0.01% | 20 |
| chr20 | 8218 | 0.01% | 23 |
| chr21 | 8718 | 0.02% | 24 |
| chr22 | 862 | <0.01% | 3 |
| chrM | 12993 | 78.42% | 7 |
| chrX | 40819 | 0.03% | 120 |
| chrY | 999 | <0.01% | 3 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 1678 | 190 | 7069 | 348.35 | 322 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF273GGC.bed.gz | 34.41 KB | e134a344512de1135ce9460e4a8046d2 |
| ENCFF273GGC.tabix.bed.gz | 17.92 KB | ba6ea8035d911463d5a944d5429ac021 |
| ENCFF273GGC.tabix.bed.gz.tbi | 22.23 KB | 385c3527f05692fd1d9a8c8de19dc74d |
| genomic_resource.yaml | 3.7 KB | 91d28fd8fff1d6abceea4cee562487b7 |
| statistics/ |