Resource
| Id | Histone_ChIP-seq/ENCSR267UCE |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR267UCE [biosample_summary="Homo sapiens Loucy" and target="H3F3A"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN700WNB|/analyses/ENCAN700WNB/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF154PDL|/files/ENCFF154PDL/} processed by ChIP-seq ENCODE3 hg19 pipeline has 41052231 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-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 {ENCFF627OZV|/files/ENCFF627OZV/} processed by ChIP-seq ENCODE3 hg19 pipeline has 35335213 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3F3A-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 {ENCFF154PDL|/files/ENCFF154PDL/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF154PDL|/files/ENCFF154PDL/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.29. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR267UCE | float |
Histone_ChIP-seq_ENCSR267UCE |
Histone_ChIP-seq ENCSR267UCE [biosample_summary="Homo sapiens Loucy" and target="H3F3A"]
|
 |
[1.55, 10.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9970736 | 0.31% | 22252 |
| chr1 | 1101308 | 0.44% | 2423 |
| chr2 | 824559 | 0.34% | 1886 |
| chr3 | 779862 | 0.39% | 1672 |
| chr4 | 443739 | 0.23% | 1024 |
| chr5 | 407140 | 0.22% | 916 |
| chr6 | 689125 | 0.40% | 1542 |
| chr7 | 429955 | 0.27% | 979 |
| chr8 | 353514 | 0.24% | 796 |
| chr9 | 418662 | 0.30% | 924 |
| chr10 | 511581 | 0.38% | 1096 |
| chr11 | 494053 | 0.37% | 1070 |
| chr12 | 533533 | 0.40% | 1231 |
| chr13 | 278437 | 0.24% | 653 |
| chr14 | 393844 | 0.37% | 845 |
| chr15 | 377353 | 0.37% | 845 |
| chr16 | 213106 | 0.24% | 487 |
| chr17 | 519459 | 0.62% | 1187 |
| chr18 | 195311 | 0.24% | 435 |
| chr19 | 262897 | 0.45% | 609 |
| chr20 | 243933 | 0.38% | 553 |
| chr21 | 145495 | 0.31% | 296 |
| chr22 | 200286 | 0.39% | 447 |
| chrX | 153584 | 0.10% | 336 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 22252 | 150 | 3896 | 448.08 | 372 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF480UVM.bed.gz | 518.81 KB | 1f0fcdc809730abab3bd14a86c11bc7d |
| ENCFF480UVM.tabix.bed.gz | 237.24 KB | 25d04457675097c3755436bf1b632906 |
| ENCFF480UVM.tabix.bed.gz.tbi | 121.06 KB | 1fc88e74d7d588bbde27fd3a2d5e21e4 |
| genomic_resource.yaml | 3.63 KB | a2c9befef465b2452e4476ac2b433769 |
| statistics/ |