Resource
| Id | DNase-seq/ENCSR000EKV |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR000EKV [biosample_summary="Homo sapiens MCF-7"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: peaks audit_internal_action: Released analysis {ENCAN487ZIT|/analyses/ENCAN487ZIT/} has in progress subobject document {b97d08b9-9a55-43de-b9d5-7a8aa2ebcb15|/documents/b97d08b9-9a55-43de-b9d5-7a8aa2ebcb15/} audit_warning: Signal Portion of Tags (SPOT) is a measure of enrichment, analogous to the commonly used fraction of reads in peaks metric. ENCODE processed alignment files {ENCFF180IVB|/files/ENCFF180IVB/} processed by DNase-seq ENCODE4 v3.0.0 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.37. According to ENCODE standards, SPOT1 score of 0.4 or higher is considered a product of high quality data. Any sample with a SPOT1 score <0.3 should be targeted for replacement with a higher quality sample, and a SPOT1 score of 0.25 is considered minimally acceptable SPOT1 score of 0.25 is considered minimally acceptable for rare and hard to find primary tissues. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR000EKV | float |
DNase-seq_ENCSR000EKV |
DNase-seq ENCSR000EKV [biosample_summary="Homo sapiens MCF-7"]
|
 |
[0.0887, 106] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 18436894 | 0.57% | 98991 |
| chr1 | 1668198 | 0.67% | 8903 |
| chr2 | 1390093 | 0.57% | 7628 |
| chr3 | 1111290 | 0.56% | 6037 |
| chr4 | 682809 | 0.36% | 3798 |
| chr5 | 886719 | 0.49% | 4873 |
| chr6 | 989953 | 0.58% | 5322 |
| chr7 | 947504 | 0.59% | 5157 |
| chr8 | 810661 | 0.56% | 4452 |
| chr9 | 810378 | 0.59% | 4342 |
| chr10 | 841422 | 0.63% | 4576 |
| chr11 | 848260 | 0.63% | 4576 |
| chr12 | 891873 | 0.67% | 4742 |
| chr13 | 365323 | 0.32% | 2022 |
| chr14 | 707618 | 0.66% | 3697 |
| chr15 | 621054 | 0.61% | 3307 |
| chr16 | 731391 | 0.81% | 3846 |
| chr17 | 1075132 | 1.29% | 5545 |
| chr18 | 291518 | 0.36% | 1621 |
| chr19 | 801982 | 1.37% | 4100 |
| chr20 | 876518 | 1.36% | 4533 |
| chr21 | 242769 | 0.52% | 1251 |
| chr22 | 336081 | 0.66% | 1806 |
| chrX | 508348 | 0.33% | 2857 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 98991 | 1 | 960 | 186.25 | 180 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF522NDW.bed.gz | 1.03 MB | b78cd610c571b09278ab2fe58fd5ec90 |
| ENCFF522NDW.tabix.bed.gz | 967.51 KB | f32fa026fe6a2853523be2c7ef1682c1 |
| ENCFF522NDW.tabix.bed.gz.tbi | 410.26 KB | 2c023f50e74e3b58fbb8069693e25a08 |
| genomic_resource.yaml | 2.12 KB | 41e8f8b25b116bd136c6b5466d7931a3 |
| statistics/ |