Resource
| Id | Histone_ChIP-seq/ENCSR075PTL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR075PTL [biosample_summary="Homo sapiens muscle layer of duodenum tissue male adult (73 years)" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (73 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN021QLF|/analyses/ENCAN021QLF/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed redacted alignments file {ENCFF801YRO|/files/ENCFF801YRO/} processed by ChIP-seq ENCODE3 hg19 pipeline has 16419881 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-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 redacted alignments file {ENCFF801YRO|/files/ENCFF801YRO/} 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 redacted alignments file {ENCFF801YRO|/files/ENCFF801YRO/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.73. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR075PTL | float |
Histone_ChIP-seq_ENCSR075PTL |
Histone_ChIP-seq ENCSR075PTL [biosample_summary="Homo sapiens muscle layer of duodenum tissue male adult (73 years)" and target="H3K4me3"]
|
 |
[1.49, 86.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 59180495 | 1.84% | 43580 |
| chr1 | 5402659 | 2.17% | 3807 |
| chr2 | 3849297 | 1.59% | 2878 |
| chr3 | 3174760 | 1.60% | 2248 |
| chr4 | 2480485 | 1.30% | 1831 |
| chr5 | 3084696 | 1.70% | 2243 |
| chr6 | 3100014 | 1.81% | 2154 |
| chr7 | 2979498 | 1.87% | 2358 |
| chr8 | 2194550 | 1.51% | 1686 |
| chr9 | 2439942 | 1.76% | 1843 |
| chr10 | 2561217 | 1.91% | 1961 |
| chr11 | 3101843 | 2.30% | 2217 |
| chr12 | 3149849 | 2.36% | 2276 |
| chr13 | 1155010 | 1.01% | 881 |
| chr14 | 1790772 | 1.67% | 1268 |
| chr15 | 1891775 | 1.85% | 1389 |
| chr16 | 2209961 | 2.45% | 1651 |
| chr17 | 3028073 | 3.64% | 2125 |
| chr18 | 939355 | 1.17% | 740 |
| chr19 | 5706433 | 9.74% | 4207 |
| chr20 | 1410173 | 2.19% | 1050 |
| chr21 | 663271 | 1.42% | 539 |
| chr22 | 1198506 | 2.36% | 910 |
| chrX | 1584425 | 1.02% | 1242 |
| chrY | 83931 | 0.15% | 76 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 43580 | 250 | 33820 | 1357.97 | 957 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF088VQH.bed.gz | 1.04 MB | 4d13a90bd62dd93e3e64a513e04bafd2 |
| ENCFF088VQH.tabix.bed.gz | 476.29 KB | ad65817a1408da451501bf9668dd7433 |
| ENCFF088VQH.tabix.bed.gz.tbi | 214.47 KB | af77354316d655f5b7c2c59aa6e10507 |
| genomic_resource.yaml | 3.29 KB | eb0ec636c497bda9f64455a05545e2a9 |
| statistics/ |