Resource
| Id | Histone_ChIP-seq/ENCSR490YCL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR490YCL [biosample_summary="Homo sapiens spleen tissue male adult (34 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (34 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN453FIE|/analyses/ENCAN453FIE/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF677QFG|/files/ENCFF677QFG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 20756432 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me1-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 {ENCFF677QFG|/files/ENCFF677QFG/} processed by ChIP-seq ENCODE3 GRCh38 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 {ENCFF677QFG|/files/ENCFF677QFG/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.39. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR490YCL | float |
Histone_ChIP-seq_ENCSR490YCL |
Histone_ChIP-seq ENCSR490YCL [biosample_summary="Homo sapiens spleen tissue male adult (34 years)" and target="H3K4me1"]
|
 |
[1.89, 70.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 58003258 | 1.80% | 125684 |
| chr1 | 5713905 | 2.30% | 12431 |
| chr1_KI270712v1_random | 411 | 0.23% | 1 |
| chr1_KI270713v1_random | 364 | 0.89% | 1 |
| chr2 | 4152233 | 1.71% | 9571 |
| chr3 | 3069648 | 1.55% | 7112 |
| chr4 | 1486810 | 0.78% | 3562 |
| chr5 | 2294742 | 1.26% | 5263 |
| chr6 | 2386008 | 1.40% | 5821 |
| chr7 | 2494241 | 1.57% | 5801 |
| chr8 | 2135644 | 1.47% | 4871 |
| chr9 | 2921694 | 2.11% | 5909 |
| chr9_KI270718v1_random | 263 | 0.69% | 1 |
| chr10 | 2945334 | 2.20% | 6427 |
| chr11 | 3632529 | 2.69% | 7480 |
| chr12 | 2470102 | 1.85% | 5475 |
| chr13 | 965908 | 0.84% | 2462 |
| chr14 | 2072577 | 1.94% | 4415 |
| chr14_KI270722v1_random | 341 | 0.18% | 1 |
| chr15 | 2024285 | 1.98% | 4431 |
| chr16 | 2923951 | 3.24% | 5779 |
| chr17 | 4136701 | 4.97% | 8079 |
| chr17_GL000205v2_random | 1694 | 0.91% | 3 |
| chr18 | 914629 | 1.14% | 2316 |
| chr19 | 3697842 | 6.31% | 6823 |
| chr20 | 2115742 | 3.28% | 4584 |
| chr21 | 765802 | 1.64% | 1717 |
| chr22 | 2205985 | 4.34% | 4229 |
| chrUn_GL000219v1 | 1853 | 1.03% | 3 |
| chrUn_KI270442v1 | 851 | 0.22% | 2 |
| chrX | 465713 | 0.30% | 1096 |
| chrY | 5456 | 0.01% | 18 |
| 3335 contigs with no values (127871343 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 125684 | 140 | 10114 | 461.5 | 353 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF031QWK.bed.gz | 2.41 MB | 50a8185d3f91b64507a8c86131fcdc65 |
| ENCFF031QWK.tabix.bed.gz | 1.19 MB | b671b1f15d000646b8dbe38427f1b91e |
| ENCFF031QWK.tabix.bed.gz.tbi | 310.13 KB | f401f80bb0e50fa628ba9e46f8bf3f10 |
| genomic_resource.yaml | 3.22 KB | f7698a8f2e2fdecb59ee06127edc3c00 |
| statistics/ |