Resource
| Id | Histone_ChIP-seq/ENCSR493FIV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR493FIV [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H3K79me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: female embryo (5 days) output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN466MYD|/analyses/ENCAN466MYD/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF518AQW|/files/ENCFF518AQW/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 35941089 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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: Processed alignments file {ENCFF033JLQ|/files/ENCFF033JLQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 41356901 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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 {ENCFF033JLQ|/files/ENCFF033JLQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.86. 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 {ENCFF033JLQ|/files/ENCFF033JLQ/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 7.01. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR493FIV | float |
Histone_ChIP-seq_ENCSR493FIV |
Histone_ChIP-seq ENCSR493FIV [biosample_summary="Homo sapiens smooth muscle cell originated from H9" and target="H3K79me2"]
|
 |
[1.28, 14] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 141684842 | 4.40% | 91539 |
| chr1 | 13688681 | 5.50% | 8761 |
| chr2 | 11637489 | 4.81% | 7239 |
| chr3 | 10235194 | 5.16% | 6408 |
| chr4 | 7026213 | 3.69% | 4617 |
| chr5 | 8052304 | 4.44% | 5129 |
| chr6 | 7653882 | 4.48% | 5196 |
| chr7 | 7343918 | 4.61% | 4858 |
| chr8 | 6220485 | 4.29% | 3753 |
| chr9 | 5889194 | 4.26% | 4172 |
| chr10 | 6983112 | 5.22% | 4657 |
| chr11 | 7132634 | 5.28% | 4804 |
| chr12 | 7407260 | 5.56% | 4698 |
| chr13 | 3599524 | 3.15% | 2364 |
| chr14 | 4936041 | 4.61% | 3019 |
| chr15 | 5177344 | 5.08% | 3239 |
| chr16 | 4445411 | 4.92% | 2896 |
| chr17 | 6461345 | 7.76% | 4165 |
| chr18 | 3382348 | 4.21% | 2320 |
| chr19 | 4603723 | 7.85% | 2997 |
| chr20 | 3263979 | 5.06% | 1875 |
| chr21 | 1505677 | 3.22% | 865 |
| chr22 | 2728752 | 5.37% | 1604 |
| chrUn_GL000195v1 | 4253 | 2.33% | 4 |
| chrUn_KI270466v1 | 353 | 28.63% | 1 |
| chrUn_KI270467v1 | 1247 | 31.81% | 2 |
| chrX | 2304479 | 1.48% | 1896 |
| 3340 contigs with no values (186116451 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 91539 | 180 | 79261 | 1547.81 | 731 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF304JWR.bed.gz | 2.02 MB | 552c233385db535205178899a5ed3dba |
| ENCFF304JWR.tabix.bed.gz | 955.78 KB | 7f05bd83446d92bf9c98dc40c7b13a37 |
| ENCFF304JWR.tabix.bed.gz.tbi | 140.88 KB | 993b840fc2dedcc4a42b9ed7f567b20d |
| genomic_resource.yaml | 3.72 KB | 847935308538bc6d7912db91e02d9004 |
| statistics/ |