Resource
| Id | Histone_ChIP-seq/ENCSR501JET |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR501JET [biosample_summary="Homo sapiens mesenchymal stem cell originated from H1" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male embryo output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN524AKT|/analyses/ENCAN524AKT/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN524AKT|/analyses/ENCAN524AKT/} has in progress subobject document {ea485615-c8dc-47fc-82c9-78d54416c641|/documents/ea485615-c8dc-47fc-82c9-78d54416c641/} audit_not_compliant: Processed alignments file {ENCFF126MVV|/files/ENCFF126MVV/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 9294981 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed alignments file {ENCFF655EKU|/files/ENCFF655EKU/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline has 13480637 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF655EKU|/files/ENCFF655EKU/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF655EKU|/files/ENCFF655EKU/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.56. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR501JET | float |
Histone_ChIP-seq_ENCSR501JET |
Histone_ChIP-seq ENCSR501JET [biosample_summary="Homo sapiens mesenchymal stem cell originated from H1" and target="H3K4me3"]
|
 |
[1.94, 100] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 22298456 | 0.69% | 35256 |
| chr1 | 2122826 | 0.85% | 3364 |
| chr2 | 1502367 | 0.62% | 2419 |
| chr3 | 1196277 | 0.60% | 1840 |
| chr4 | 884262 | 0.46% | 1241 |
| chr5 | 1021933 | 0.56% | 1631 |
| chr6 | 1217900 | 0.71% | 1855 |
| chr7 | 1131555 | 0.71% | 1846 |
| chr8 | 856496 | 0.59% | 1350 |
| chr9 | 956429 | 0.69% | 1494 |
| chr10 | 941192 | 0.70% | 1558 |
| chr11 | 1222647 | 0.91% | 1960 |
| chr12 | 1096954 | 0.82% | 1646 |
| chr13 | 455808 | 0.40% | 724 |
| chr14 | 708969 | 0.66% | 1128 |
| chr15 | 705294 | 0.69% | 1132 |
| chr16 | 982289 | 1.09% | 1548 |
| chr17 | 1360831 | 1.63% | 2118 |
| chr18 | 389225 | 0.48% | 610 |
| chr19 | 1521955 | 2.60% | 2497 |
| chr20 | 606917 | 0.94% | 1026 |
| chr21 | 226782 | 0.49% | 397 |
| chr22 | 552770 | 1.09% | 958 |
| chrX | 619736 | 0.40% | 887 |
| chrY | 17042 | 0.03% | 27 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 35256 | 108 | 5960 | 632.47 | 417 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF570CII.bed.gz | 891.59 KB | 3885900330ac6198669152d8c891c318 |
| ENCFF570CII.tabix.bed.gz | 388.05 KB | 34c9b005458b1107920a5e1d1ffa8d9d |
| ENCFF570CII.tabix.bed.gz.tbi | 181.47 KB | c1f250f69d7f69636ae33e9fbc5ab0d3 |
| genomic_resource.yaml | 3.95 KB | 2bdbe340ab99a72171e5be70d62b3438 |
| statistics/ |