Resource
| Id | Histone_ChIP-seq/ENCSR967HXD |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR967HXD [biosample_summary="Homo sapiens H9 stably expressing HES5" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: stably expressing C-terminal eGFP-tagged HES5 output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN240BQK|/analyses/ENCAN240BQK/} has in progress subobject document {cf44fa62-50ae-4eb1-aeb9-6403fd645dee|/documents/cf44fa62-50ae-4eb1-aeb9-6403fd645dee/} audit_internal_action: Released analysis {ENCAN240BQK|/analyses/ENCAN240BQK/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF695XNX|/files/ENCFF695XNX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 34215070 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: Processed alignments file {ENCFF418IUS|/files/ENCFF418IUS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 35789340 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 {ENCFF695XNX|/files/ENCFF695XNX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 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 alignments file {ENCFF695XNX|/files/ENCFF695XNX/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 7.98. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR967HXD | float |
Histone_ChIP-seq_ENCSR967HXD |
Histone_ChIP-seq ENCSR967HXD [biosample_summary="Homo sapiens H9 stably expressing HES5" and target="H3K4me1"]
|
 |
[1.57, 8.83] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 62364350 | 1.94% | 86326 |
| chr1 | 6140293 | 2.47% | 8221 |
| chr2 | 4794761 | 1.98% | 6726 |
| chr3 | 4005794 | 2.02% | 5655 |
| chr4 | 2717891 | 1.43% | 4000 |
| chr5 | 3392356 | 1.87% | 4715 |
| chr6 | 3666390 | 2.15% | 5144 |
| chr7 | 3215620 | 2.02% | 4552 |
| chr8 | 2685483 | 1.85% | 3813 |
| chr9 | 2863813 | 2.07% | 3904 |
| chr10 | 3107167 | 2.32% | 4287 |
| chr11 | 3558219 | 2.63% | 4785 |
| chr12 | 3010336 | 2.26% | 4212 |
| chr13 | 1539430 | 1.35% | 2221 |
| chr14 | 2019235 | 1.89% | 2831 |
| chr15 | 2213899 | 2.17% | 2944 |
| chr16 | 2230661 | 2.47% | 2998 |
| chr17 | 3107474 | 3.73% | 4028 |
| chr18 | 1467459 | 1.83% | 2081 |
| chr19 | 1967896 | 3.36% | 2755 |
| chr20 | 1770782 | 2.75% | 2403 |
| chr21 | 642929 | 1.38% | 886 |
| chr22 | 1447292 | 2.85% | 1917 |
| chrX | 799170 | 0.51% | 1248 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 86326 | 193 | 8633 | 722.43 | 602 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF731UCU.bed.gz | 1.86 MB | 273a306191ae4a30033898177b3fe631 |
| ENCFF731UCU.tabix.bed.gz | 902.99 KB | e665736febc0de293a666a5b52914883 |
| ENCFF731UCU.tabix.bed.gz.tbi | 322.39 KB | 7d7800addde9b1849f7422931debd8ee |
| genomic_resource.yaml | 3.96 KB | 7f2f1a820f84ae87be4a789adffa835c |
| statistics/ |