Resource
| Id | Histone_ChIP-seq/ENCSR000AQQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AQQ [biosample_summary="Homo sapiens astrocyte" and target="H3K79me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN866XGP|/analyses/ENCAN866XGP/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF490VHZ|/files/ENCFF490VHZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 15723809 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_not_compliant: Processed alignments file {ENCFF169JQT|/files/ENCFF169JQT/} processed by ChIP-seq ENCODE3 hg19 pipeline has 26810495 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 {ENCFF490VHZ|/files/ENCFF490VHZ/} 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 {ENCFF490VHZ|/files/ENCFF490VHZ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.21. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AQQ | float |
Histone_ChIP-seq_ENCSR000AQQ |
Histone_ChIP-seq ENCSR000AQQ [biosample_summary="Homo sapiens astrocyte" and target="H3K79me2"]
|
 |
[1.76, 28.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 134436726 | 4.18% | 147660 |
| chr1 | 12648944 | 5.08% | 13950 |
| chr2 | 10117513 | 4.18% | 10543 |
| chr3 | 9480579 | 4.78% | 9747 |
| chr4 | 6157682 | 3.24% | 6686 |
| chr5 | 7553771 | 4.16% | 7776 |
| chr6 | 6815482 | 3.99% | 7263 |
| chr7 | 7017677 | 4.40% | 7956 |
| chr8 | 5736665 | 3.95% | 5930 |
| chr9 | 5768564 | 4.17% | 6372 |
| chr10 | 6940997 | 5.19% | 7777 |
| chr11 | 6541810 | 4.84% | 7237 |
| chr12 | 7078307 | 5.31% | 7736 |
| chr13 | 3592241 | 3.14% | 3759 |
| chr14 | 4612465 | 4.31% | 5273 |
| chr15 | 5114873 | 5.02% | 5521 |
| chr16 | 4757751 | 5.27% | 5542 |
| chr17 | 6457335 | 7.76% | 7668 |
| chr18 | 2731678 | 3.40% | 3121 |
| chr19 | 4932853 | 8.42% | 5892 |
| chr20 | 3305217 | 5.13% | 3478 |
| chr21 | 1464036 | 3.13% | 1623 |
| chr22 | 3019213 | 5.94% | 3375 |
| chrX | 2426523 | 1.56% | 3234 |
| chrY | 164550 | 0.29% | 201 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 147660 | 130 | 30020 | 910.45 | 509 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF100ZHU.bed.gz | 3.36 MB | 6a54a7cd2302b03a0d4245583625cb00 |
| ENCFF100ZHU.tabix.bed.gz | 1.49 MB | 20fc3a5b785b25f3ae2043cfa808a955 |
| ENCFF100ZHU.tabix.bed.gz.tbi | 149.27 KB | 2f3b5103eeb840d23215f5ea706cfaf5 |
| genomic_resource.yaml | 3.68 KB | 91f781bf817d004537757a182dd0ff2e |
| statistics/ |