Resource
| Id | Histone_ChIP-seq/ENCSR000ANB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ANB [biosample_summary="Homo sapiens H1" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN652GDW|/analyses/ENCAN652GDW/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF097LJG|/files/ENCFF097LJG/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 11157638 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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_not_compliant: Processed alignments file {ENCFF642ZPO|/files/ENCFF642ZPO/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline has 11094785 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-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 {ENCFF642ZPO|/files/ENCFF642ZPO/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 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 alignments file {ENCFF642ZPO|/files/ENCFF642ZPO/} processed by ChIP-seq ENCODE4 v1.8.1 GRCh38 pipeline was generated from a library with PBC2 value of 9.55. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ANB | float |
Histone_ChIP-seq_ENCSR000ANB |
Histone_ChIP-seq ENCSR000ANB [biosample_summary="Homo sapiens H1" and target="H3K36me3"]
|
 |
[2.17, 18.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 41520089 | 1.29% | 70548 |
| chr1 | 4536238 | 1.82% | 7280 |
| chr2 | 2875876 | 1.19% | 5078 |
| chr3 | 2346907 | 1.18% | 4102 |
| chr4 | 1443422 | 0.76% | 2725 |
| chr5 | 2091160 | 1.15% | 3674 |
| chr6 | 1855026 | 1.09% | 3261 |
| chr7 | 1872513 | 1.18% | 3250 |
| chr8 | 1224647 | 0.84% | 2162 |
| chr9 | 1767508 | 1.28% | 2962 |
| chr10 | 1626657 | 1.22% | 2883 |
| chr11 | 2331671 | 1.73% | 3798 |
| chr12 | 2567736 | 1.93% | 4098 |
| chr13 | 655902 | 0.57% | 1314 |
| chr14 | 1328656 | 1.24% | 2313 |
| chr15 | 1447361 | 1.42% | 2498 |
| chr16 | 1992167 | 2.21% | 3252 |
| chr17 | 2628885 | 3.16% | 4181 |
| chr18 | 565799 | 0.70% | 1183 |
| chr19 | 2707919 | 4.62% | 4390 |
| chr20 | 1390523 | 2.16% | 2160 |
| chr21 | 496238 | 1.06% | 844 |
| chr22 | 1189475 | 2.34% | 1867 |
| chrX | 550996 | 0.35% | 1209 |
| chrY | 26807 | 0.05% | 64 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 70548 | 158 | 12150 | 588.54 | 438 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF504KOV.bed.gz | 1.44 MB | 9d5c70f06a9b493863fc2f386eb08d27 |
| ENCFF504KOV.tabix.bed.gz | 708.25 KB | 33a7404a0f3bd8388b8f29878638e879 |
| ENCFF504KOV.tabix.bed.gz.tbi | 138.83 KB | 31376d8d6731866c90cece235111237f |
| genomic_resource.yaml | 3.7 KB | 5bf050ba7572acc0e49382c54a13c5e1 |
| statistics/ |