Resource
| Id | DNase-seq/ENCSR563XRP |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR563XRP [biosample_summary="Homo sapiens large intestine tissue female embryo (107 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female embryo (107 days) output_type: peaks audit_warning: Alignment file {ENCFF481MBB|/files/ENCFF481MBB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ( {ENCPL848KLD|/pipelines/ENCPL848KLD/} ) for GRCh38 assembly has 20920971 mapped reads. According to ENCODE standards, conventional DNase-seq profile requires a minimum of 20 million uniquely mapped reads to generate a reliable SPOT (Signal Portion of Tags) score. The recommended value is > 50 million. For deep, foot-printing depth DNase-seq 150-200 million uniquely mapped reads are recommended. (See {ENCODE DNase-seq data standards|/data-standards/dnase-seq-encode4/}) 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 {ENCFF481MBB|/files/ENCFF481MBB/} processed by DNase-seq ENCODE4 v3.0.0-alpha.2 GRCh38 pipeline ({ENCPL848KLD|/pipelines/ENCPL848KLD/}) for GRCh38 assembly have a SPOT1 score of 0.35. 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_ENCSR563XRP | float |
DNase-seq_ENCSR563XRP |
DNase-seq ENCSR563XRP [biosample_summary="Homo sapiens large intestine tissue female embryo (107 days)"]
|
 |
[0.336, 20.7] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 7051574 | 0.22% | 41148 |
| chr1 | 677304 | 0.27% | 3934 |
| chr2 | 568850 | 0.23% | 3343 |
| chr3 | 470345 | 0.24% | 2761 |
| chr4 | 386740 | 0.20% | 2246 |
| chr5 | 375803 | 0.21% | 2208 |
| chr6 | 436070 | 0.26% | 2517 |
| chr7 | 371082 | 0.23% | 2167 |
| chr8 | 297452 | 0.20% | 1754 |
| chr9 | 285240 | 0.21% | 1671 |
| chr10 | 311242 | 0.23% | 1851 |
| chr11 | 363646 | 0.27% | 2131 |
| chr12 | 369707 | 0.28% | 2169 |
| chr13 | 181521 | 0.16% | 1081 |
| chr14 | 231177 | 0.22% | 1332 |
| chr15 | 213387 | 0.21% | 1256 |
| chr16 | 235386 | 0.26% | 1357 |
| chr17 | 270663 | 0.33% | 1591 |
| chr18 | 171481 | 0.21% | 1003 |
| chr19 | 270372 | 0.46% | 1471 |
| chr20 | 175339 | 0.27% | 1009 |
| chr21 | 75419 | 0.16% | 442 |
| chr22 | 121963 | 0.24% | 709 |
| chrX | 191085 | 0.12% | 1143 |
| chrY | 300 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 41148 | 2 | 680 | 171.37 | 176 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF632ETC.bed.gz | 435.94 KB | 2590f593a5704a88ac0dd93b88d70c34 |
| ENCFF632ETC.tabix.bed.gz | 382.91 KB | 8e986c163d80bbe3577661f6024de5c1 |
| ENCFF632ETC.tabix.bed.gz.tbi | 256.51 KB | 845a2fc64f23a1cd33aadc4477d2efe7 |
| genomic_resource.yaml | 2.68 KB | 0d768495e827da98cbdb4c6c9d965abd |
| statistics/ |