Resource
| Id | Histone_ChIP-seq/ENCSR000ATH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000ATH [biosample_summary="Homo sapiens osteoblast" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 2, Rep 3 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN872QNS|/analyses/ENCAN872QNS/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF164SGX|/files/ENCFF164SGX/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 8095546 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 {ENCFF877XAA|/files/ENCFF877XAA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 16452393 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 {ENCFF877XAA|/files/ENCFF877XAA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF877XAA|/files/ENCFF877XAA/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 6.17. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000ATH | float |
Histone_ChIP-seq_ENCSR000ATH |
Histone_ChIP-seq ENCSR000ATH [biosample_summary="Homo sapiens osteoblast" and target="H3K4me3"]
|
 |
[1.78, 94] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 48082505 | 1.49% | 44817 |
| chr1 | 4585702 | 1.84% | 4113 |
| chr2 | 3488478 | 1.44% | 3445 |
| chr3 | 2798045 | 1.41% | 2640 |
| chr4 | 2090589 | 1.10% | 2073 |
| chr5 | 2477561 | 1.36% | 2402 |
| chr6 | 3035166 | 1.78% | 2865 |
| chr7 | 2362100 | 1.48% | 2265 |
| chr8 | 1933539 | 1.33% | 1911 |
| chr9 | 1986387 | 1.44% | 1864 |
| chr10 | 2167553 | 1.62% | 2167 |
| chr11 | 2542485 | 1.88% | 2213 |
| chr12 | 2599990 | 1.95% | 2386 |
| chr13 | 1099628 | 0.96% | 1145 |
| chr14 | 1509921 | 1.41% | 1345 |
| chr14_GL000194v1_random | 193 | 0.10% | 1 |
| chr15 | 1590217 | 1.56% | 1484 |
| chr16 | 1776430 | 1.97% | 1584 |
| chr17 | 2586365 | 3.11% | 2293 |
| chr17_GL000205v2_random | 2116 | 1.14% | 2 |
| chr18 | 885922 | 1.10% | 924 |
| chr19 | 2589593 | 4.42% | 2095 |
| chr20 | 1177506 | 1.83% | 1110 |
| chr21 | 510342 | 1.09% | 531 |
| chr22 | 975455 | 1.92% | 872 |
| chrUn_GL000195v1 | 639 | 0.35% | 2 |
| chrUn_GL000219v1 | 2442 | 1.36% | 3 |
| chrUn_GL000220v1 | 517 | 0.32% | 2 |
| chrX | 1307624 | 0.84% | 1080 |
| 3338 contigs with no values (185403544 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 44817 | 190 | 21117 | 1072.86 | 621 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF261AED.bed.gz | 1.13 MB | 15b00e00c9c041403803dd8dee0027ed |
| ENCFF261AED.tabix.bed.gz | 502.72 KB | 24cee5f451510048850bf6a324a6e34b |
| ENCFF261AED.tabix.bed.gz.tbi | 235.83 KB | c1ab7aaced9b3a4ebaa096e3fcf088d7 |
| genomic_resource.yaml | 3.68 KB | 1eea0c468ea2fe2fb14a68c8453dd303 |
| statistics/ |