Resource
| Id | Histone_ChIP-seq/ENCSR000AOH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000AOH [biosample_summary="Homo sapiens HeLa-S3" and target="H3K9ac"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN728PEP|/analyses/ENCAN728PEP/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF203MBP|/files/ENCFF203MBP/} processed by ChIP-seq ENCODE3 hg19 pipeline has 14506406 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 {ENCFF112SRH|/files/ENCFF112SRH/} processed by ChIP-seq ENCODE3 hg19 pipeline has 16167716 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 {ENCFF203MBP|/files/ENCFF203MBP/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF203MBP|/files/ENCFF203MBP/} 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_ENCSR000AOH | float |
Histone_ChIP-seq_ENCSR000AOH |
Histone_ChIP-seq ENCSR000AOH [biosample_summary="Homo sapiens HeLa-S3" and target="H3K9ac"]
|
 |
[1.35, 171] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 45171532 | 1.40% | 38801 |
| chr1 | 4578576 | 1.84% | 3882 |
| chr2 | 2786690 | 1.15% | 2400 |
| chr3 | 2373152 | 1.20% | 1977 |
| chr4 | 1204449 | 0.63% | 1015 |
| chr5 | 1940220 | 1.07% | 1653 |
| chr6 | 2408870 | 1.41% | 1958 |
| chr7 | 1943822 | 1.22% | 1720 |
| chr8 | 1633520 | 1.13% | 1431 |
| chr9 | 2272740 | 1.64% | 2044 |
| chr10 | 1938206 | 1.45% | 1692 |
| chr11 | 2703932 | 2.00% | 2243 |
| chr12 | 2498078 | 1.87% | 1980 |
| chr13 | 690746 | 0.60% | 632 |
| chr14 | 1540485 | 1.44% | 1262 |
| chr15 | 1602042 | 1.57% | 1357 |
| chr16 | 2053346 | 2.27% | 1910 |
| chr17 | 3041643 | 3.65% | 2586 |
| chr18 | 762404 | 0.95% | 651 |
| chr19 | 2840395 | 4.85% | 2541 |
| chr20 | 1439535 | 2.23% | 1336 |
| chr21 | 617949 | 1.32% | 538 |
| chr22 | 1076195 | 2.12% | 994 |
| chrX | 1223798 | 0.78% | 998 |
| chrY | 739 | <0.01% | 1 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38801 | 220 | 13630 | 1164.18 | 757 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF723WDR.bed.gz | 964.82 KB | cee84fa1f78de5416de2caa2c87ca634 |
| ENCFF723WDR.tabix.bed.gz | 425.11 KB | ff28033ce27ec7bd29c7d61098db1116 |
| ENCFF723WDR.tabix.bed.gz.tbi | 164.22 KB | f7bf1406102eaa53f75ba150792153f6 |
| genomic_resource.yaml | 3.65 KB | 3fb2a493f58666a165e6aabf9ced43d1 |
| statistics/ |