Resource
| Id | Histone_ChIP-seq/ENCSR000AMD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AMD [biosample_summary="Homo sapiens HepG2" and target="H3K9ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN607QWC|/analyses/ENCAN607QWC/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF194LQS|/files/ENCFF194LQS/} processed by ChIP-seq ENCODE3 hg19 pipeline has 5184585 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9ac-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed alignments file {ENCFF243VAM|/files/ENCFF243VAM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 12883462 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9ac-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF194LQS|/files/ENCFF194LQS/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF194LQS|/files/ENCFF194LQS/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 6.06. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000AMD | float |
Histone_ChIP-seq_ENCSR000AMD |
Histone_ChIP-seq ENCSR000AMD [biosample_summary="Homo sapiens HepG2" and target="H3K9ac"]
|
 |
[1.81, 95.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 49376871 | 1.53% | 45562 |
| chr1 | 4873535 | 1.96% | 4540 |
| chr2 | 3819450 | 1.58% | 3346 |
| chr3 | 2886312 | 1.46% | 2615 |
| chr4 | 1695567 | 0.89% | 1523 |
| chr5 | 2176313 | 1.20% | 1965 |
| chr6 | 2897859 | 1.70% | 2505 |
| chr7 | 2189588 | 1.37% | 2116 |
| chr8 | 1807412 | 1.25% | 1646 |
| chr9 | 2062222 | 1.49% | 1939 |
| chr10 | 2101978 | 1.57% | 1965 |
| chr11 | 2476134 | 1.83% | 2207 |
| chr12 | 2380782 | 1.79% | 2150 |
| chr13 | 936315 | 0.82% | 870 |
| chr14 | 1737744 | 1.62% | 1527 |
| chr15 | 1443991 | 1.42% | 1366 |
| chr16 | 2333248 | 2.58% | 2208 |
| chr17 | 3181190 | 3.82% | 2925 |
| chr18 | 848707 | 1.06% | 794 |
| chr19 | 2799057 | 4.78% | 2769 |
| chr20 | 1636403 | 2.54% | 1477 |
| chr21 | 595328 | 1.27% | 586 |
| chr22 | 1273861 | 2.51% | 1250 |
| chrM | 333 | 2.01% | 1 |
| chrX | 1184035 | 0.76% | 1230 |
| chrY | 39507 | 0.07% | 42 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 45562 | 195 | 14146 | 1083.73 | 715 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF441EPA.bed.gz | 1.15 MB | 7ab093e8d5dfbb9ff13fe8314c9cf790 |
| ENCFF441EPA.tabix.bed.gz | 507.96 KB | d114c5ad8dca88c15e1fc11dc71a5ea8 |
| ENCFF441EPA.tabix.bed.gz.tbi | 169.57 KB | 44071946dad2c5bc3889b31b2a3b3ade |
| genomic_resource.yaml | 3.76 KB | 8c70a8cbbb17c026b1bf0f11e98f275f |
| statistics/ |