Resource
| Id | Histone_ChIP-seq/ENCSR940FNL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR940FNL [biosample_summary="Homo sapiens tibial artery tissue male adult (54 years)" and target="H3K27me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (54 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN032LIN|/analyses/ENCAN032LIN/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF351JIG|/files/ENCFF351JIG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 42593685 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 alignments file {ENCFF351JIG|/files/ENCFF351JIG/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF351JIG|/files/ENCFF351JIG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.07. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR940FNL | float |
Histone_ChIP-seq_ENCSR940FNL |
Histone_ChIP-seq ENCSR940FNL [biosample_summary="Homo sapiens tibial artery tissue male adult (54 years)" and target="H3K27me3"]
|
 |
[1.57, 10.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 20931455 | 0.65% | 18704 |
| chr1 | 2241926 | 0.90% | 2143 |
| chr1_KI270712v1_random | 4916 | 2.79% | 8 |
| chr1_KI270713v1_random | 4887 | 11.99% | 3 |
| chr1_KI270714v1_random | 332 | 0.80% | 1 |
| chr2 | 1354614 | 0.56% | 1114 |
| chr3 | 761964 | 0.38% | 708 |
| chr4 | 659187 | 0.35% | 549 |
| chr5 | 844832 | 0.47% | 725 |
| chr6 | 1222707 | 0.72% | 1062 |
| chr7 | 1123682 | 0.71% | 934 |
| chr8 | 689986 | 0.48% | 616 |
| chr9 | 1027284 | 0.74% | 911 |
| chr9_KI270717v1_random | 290 | 0.72% | 1 |
| chr10 | 1002466 | 0.75% | 898 |
| chr11 | 1023318 | 0.76% | 972 |
| chr12 | 886495 | 0.67% | 865 |
| chr13 | 384609 | 0.34% | 301 |
| chr14 | 596474 | 0.56% | 500 |
| chr15 | 612804 | 0.60% | 557 |
| chr16 | 808813 | 0.90% | 733 |
| chr17 | 1849520 | 2.22% | 1634 |
| chr17_GL000205v2_random | 7108 | 3.83% | 7 |
| chr18 | 266796 | 0.33% | 267 |
| chr19 | 1734443 | 2.96% | 1424 |
| chr20 | 901012 | 1.40% | 870 |
| chr21 | 217431 | 0.47% | 196 |
| chr22 | 604806 | 1.19% | 600 |
| chr22_KI270733v1_random | 1363 | 0.76% | 2 |
| chrUn_GL000195v1 | 396 | 0.22% | 1 |
| chrUn_GL000219v1 | 1083 | 0.60% | 2 |
| chrUn_GL000224v1 | 1117 | 0.62% | 2 |
| chrUn_KI270744v1 | 495 | 0.29% | 1 |
| chrX | 94299 | 0.06% | 97 |
| 3333 contigs with no values (184930311 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 18704 | 235 | 21706 | 1119.09 | 770 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF763MDJ.bed.gz | 384.6 KB | 9016828b65a65c03091bd27be38909ab |
| ENCFF763MDJ.tabix.bed.gz | 193.48 KB | 2c115aa6d508488ee36220e81478ac37 |
| ENCFF763MDJ.tabix.bed.gz.tbi | 81.05 KB | 87e17999c6cb1f889146d234c0d1ed87 |
| genomic_resource.yaml | 3.24 KB | c4ede3f98023c4969c4be55656c8221f |
| statistics/ |