Resource
| Id | Histone_ChIP-seq/ENCSR298PMB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR298PMB [biosample_summary="Homo sapiens thymus tissue male child (3 years)" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male child (3 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN010JFC|/analyses/ENCAN010JFC/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed unfiltered alignments file {ENCFF283PVE|/files/ENCFF283PVE/} processed by ChIP-seq ENCODE3 hg19 pipeline has 44818649 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF430XIR|/files/ENCFF430XIR/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF430XIR|/files/ENCFF430XIR/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 7.87. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR298PMB | float |
Histone_ChIP-seq_ENCSR298PMB |
Histone_ChIP-seq ENCSR298PMB [biosample_summary="Homo sapiens thymus tissue male child (3 years)" and target="H3K9me3"]
|
 |
[1.33, 15.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5824079 | 0.18% | 40526 |
| chr1 | 342967 | 0.14% | 2508 |
| chr2 | 352692 | 0.15% | 2618 |
| chr3 | 274665 | 0.14% | 2032 |
| chr4 | 304404 | 0.16% | 2130 |
| chr5 | 303198 | 0.17% | 2208 |
| chr6 | 259250 | 0.15% | 1960 |
| chr7 | 431538 | 0.27% | 2963 |
| chr8 | 254796 | 0.18% | 1765 |
| chr9 | 178345 | 0.13% | 1302 |
| chr10 | 228721 | 0.17% | 1715 |
| chr11 | 188942 | 0.14% | 1398 |
| chr12 | 292862 | 0.22% | 1981 |
| chr13 | 195470 | 0.17% | 1471 |
| chr14 | 142835 | 0.13% | 1029 |
| chr15 | 195278 | 0.19% | 1288 |
| chr16 | 246565 | 0.27% | 1628 |
| chr17 | 198532 | 0.24% | 1393 |
| chr18 | 102521 | 0.13% | 769 |
| chr19 | 850108 | 1.45% | 4998 |
| chr20 | 140922 | 0.22% | 1027 |
| chr21 | 124909 | 0.27% | 792 |
| chr22 | 90226 | 0.18% | 644 |
| chrX | 98106 | 0.06% | 735 |
| chrY | 26227 | 0.05% | 172 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 40526 | 90 | 2396 | 143.71 | 119 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF853MVL.bed.gz | 634.6 KB | 9608c349165e15b79110eb2415d10c37 |
| ENCFF853MVL.tabix.bed.gz | 349.03 KB | 5b80101e4b2a10ba7f1c66d771cd9ef4 |
| ENCFF853MVL.tabix.bed.gz.tbi | 214.92 KB | f2343a7aee0644a054ae271c47541c02 |
| genomic_resource.yaml | 3.21 KB | 98be0da956391dc3a4cc9ef58a94b687 |
| statistics/ |