Resource
| Id | Histone_ChIP-seq/ENCSR368YAQ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR368YAQ [biosample_summary="Homo sapiens mucosa of stomach tissue male adult (59 years)" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1 summary: male adult (59 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN881DBW|/analyses/ENCAN881DBW/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF838RXS|/files/ENCFF838RXS/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline has 27211636 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 redacted alignments file {ENCFF838RXS|/files/ENCFF838RXS/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF838RXS|/files/ENCFF838RXS/} processed by ChIP-seq ENCODE4 v1.7.0 GRCh38 pipeline was generated from a library with PBC2 value of 5.27. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR368YAQ | float |
Histone_ChIP-seq_ENCSR368YAQ |
Histone_ChIP-seq ENCSR368YAQ [biosample_summary="Homo sapiens mucosa of stomach tissue male adult (59 years)" and target="H3K4me1"]
|
 |
[1.61, 21.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 101630690 | 3.16% | 104837 |
| chr1 | 10711894 | 4.30% | 10528 |
| chr2 | 8126979 | 3.36% | 8439 |
| chr3 | 6311275 | 3.18% | 6719 |
| chr4 | 4110022 | 2.16% | 4671 |
| chr5 | 5036083 | 2.77% | 5408 |
| chr6 | 5823492 | 3.41% | 6260 |
| chr7 | 4465239 | 2.80% | 4941 |
| chr8 | 4090946 | 2.82% | 4385 |
| chr9 | 4705103 | 3.40% | 4767 |
| chr10 | 5099862 | 3.81% | 5116 |
| chr11 | 5782974 | 4.28% | 5631 |
| chr12 | 4729311 | 3.55% | 5001 |
| chr13 | 2081200 | 1.82% | 2326 |
| chr14 | 3479466 | 3.25% | 3450 |
| chr15 | 3577401 | 3.51% | 3610 |
| chr16 | 3812884 | 4.22% | 3766 |
| chr17 | 5691866 | 6.84% | 5265 |
| chr18 | 1900489 | 2.36% | 2021 |
| chr19 | 3869658 | 6.60% | 3884 |
| chr20 | 3057167 | 4.74% | 3065 |
| chr21 | 1318058 | 2.82% | 1295 |
| chr22 | 2569663 | 5.06% | 2358 |
| chrX | 1231018 | 0.79% | 1841 |
| chrY | 48640 | 0.08% | 90 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 104837 | 250 | 19337 | 969.42 | 756 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF122DXE.bed.gz | 2.19 MB | eeb5cb697f19532b711cdcd8f5a82284 |
| ENCFF122DXE.tabix.bed.gz | 1.05 MB | 7e091949565675585f883f7056cc4371 |
| ENCFF122DXE.tabix.bed.gz.tbi | 299.3 KB | 64997b4e6a492022f8c75becc1adc5a0 |
| genomic_resource.yaml | 3.3 KB | 61b318c90e1754d78521f339f94a903b |
| statistics/ |