Resource
| Id | DNase-seq/ENCSR941SMM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR941SMM [biosample_summary="Homo sapiens stomach tissue embryo (101 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: embryo (101 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN462CKY|/analyses/ENCAN462CKY/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} audit_warning: Alignment file {ENCFF429HHU|/files/ENCFF429HHU/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 35121807 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/}) audit_warning: Alignment file {ENCFF348UDP|/files/ENCFF348UDP/} processed by DNase-seq ENCODE3 GRCh38 pipeline ( {ENCPL001DNS|/pipelines/ENCPL001DNS/} ) for GRCh38 assembly has 34842959 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/}) 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 {ENCFF348UDP|/files/ENCFF348UDP/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.31. 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/}) |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| DNase-seq_ENCSR941SMM | float |
DNase-seq_ENCSR941SMM |
DNase-seq ENCSR941SMM [biosample_summary="Homo sapiens stomach tissue embryo (101 days)"]
|
 |
[4, 1.36e+03] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9666239 | 0.30% | 64032 |
| chr1 | 896460 | 0.36% | 5944 |
| chr2 | 781964 | 0.32% | 5185 |
| chr3 | 623763 | 0.31% | 4128 |
| chr4 | 511224 | 0.27% | 3388 |
| chr5 | 533052 | 0.29% | 3530 |
| chr6 | 609040 | 0.36% | 4031 |
| chr7 | 513852 | 0.32% | 3397 |
| chr8 | 450516 | 0.31% | 2976 |
| chr9 | 397167 | 0.29% | 2638 |
| chr10 | 440060 | 0.33% | 2910 |
| chr11 | 476580 | 0.35% | 3164 |
| chr12 | 488453 | 0.37% | 3238 |
| chr13 | 269458 | 0.24% | 1782 |
| chr14 | 314144 | 0.29% | 2086 |
| chr15 | 310790 | 0.30% | 2059 |
| chr16 | 301894 | 0.33% | 2000 |
| chr17 | 402040 | 0.48% | 2665 |
| chr18 | 209707 | 0.26% | 1385 |
| chr19 | 364239 | 0.62% | 2419 |
| chr20 | 247377 | 0.38% | 1638 |
| chr21 | 106138 | 0.23% | 697 |
| chr22 | 157577 | 0.31% | 1043 |
| chrX | 249494 | 0.16% | 1655 |
| chrY | 11250 | 0.02% | 74 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 64032 | 12 | 572 | 150.96 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF785AIA.bed.gz | 617.75 KB | bdb97057a2b9b1a3c21a45f43498b386 |
| ENCFF785AIA.tabix.bed.gz | 529.01 KB | 653146bddfeb6a0a691f2a12ac1e42a4 |
| ENCFF785AIA.tabix.bed.gz.tbi | 320.68 KB | d2a75fa705d9f5de4619a095c3e5400d |
| genomic_resource.yaml | 3.36 KB | 7175b3172625a947e038105654c621ea |
| statistics/ |