Resource
| Id | Histone_ChIP-seq/ENCSR929AXP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR929AXP [biosample_summary="Homo sapiens muscle layer of duodenum tissue male adult (59 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (59 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN067TVG|/analyses/ENCAN067TVG/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF944EAQ|/files/ENCFF944EAQ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 32711960 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K27me3-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 redacted alignments file {ENCFF944EAQ|/files/ENCFF944EAQ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.90. 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 {ENCFF944EAQ|/files/ENCFF944EAQ/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.49. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR929AXP | float |
Histone_ChIP-seq_ENCSR929AXP |
Histone_ChIP-seq ENCSR929AXP [biosample_summary="Homo sapiens muscle layer of duodenum tissue male adult (59 years)" and target="H3K27me3"]
|
 |
[1.48, 13] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 13255403 | 0.41% | 13880 |
| chr1 | 1340941 | 0.54% | 1488 |
| chr2 | 1049707 | 0.43% | 994 |
| chr3 | 519778 | 0.26% | 545 |
| chr4 | 510164 | 0.27% | 494 |
| chr5 | 787823 | 0.43% | 783 |
| chr6 | 829323 | 0.49% | 811 |
| chr7 | 690630 | 0.43% | 614 |
| chr8 | 541202 | 0.37% | 583 |
| chr9 | 585351 | 0.42% | 593 |
| chr10 | 714200 | 0.53% | 735 |
| chr11 | 647389 | 0.48% | 715 |
| chr12 | 666202 | 0.50% | 679 |
| chr13 | 316472 | 0.28% | 334 |
| chr14 | 419042 | 0.39% | 432 |
| chr15 | 408363 | 0.40% | 446 |
| chr16 | 386799 | 0.43% | 441 |
| chr17 | 915134 | 1.10% | 955 |
| chr18 | 187193 | 0.23% | 215 |
| chr19 | 712422 | 1.22% | 798 |
| chr20 | 556971 | 0.86% | 651 |
| chr21 | 126700 | 0.27% | 135 |
| chr22 | 284280 | 0.56% | 359 |
| chrM | 987 | 5.96% | 1 |
| chrX | 57148 | 0.04% | 77 |
| chrY | 1182 | <0.01% | 2 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 13880 | 235 | 16017 | 955 | 692.5 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF456XDW.bed.gz | 270.66 KB | 3245fbee2a1da11d0bcc26c0a879ee68 |
| ENCFF456XDW.tabix.bed.gz | 140.33 KB | 0c7be239a447c460eff668b42b0c787a |
| ENCFF456XDW.tabix.bed.gz.tbi | 65.97 KB | 092e9b9b1c77deb35c65ff26d2faebe5 |
| genomic_resource.yaml | 3.3 KB | 105989e046c8e54334c1238476983e03 |
| statistics/ |