Resource
| Id | DNase-seq/ENCSR627NIF |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR627NIF [biosample_summary="Homo sapiens lung tissue male embryo (54 days) and male embryo (58 days)"] |
| Description |
status: released biological_replicates: Rep 1 summary: male embryo (58 days) male embryo (54 days) output_type: peaks audit_internal_action: Archived analysis {ENCAN157TJR|/analyses/ENCAN157TJR/} has in progress subobject quality standard {encode3-dnase|/quality-standards/encode3-dnase/} 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 {ENCFF710GMU|/files/ENCFF710GMU/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.32. 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/}) 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 {ENCFF515DYE|/files/ENCFF515DYE/} processed by DNase-seq ENCODE3 GRCh38 pipeline ({ENCPL001DNS|/pipelines/ENCPL001DNS/}) for GRCh38 assembly have a SPOT1 score of 0.29. 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_ENCSR627NIF | float |
DNase-seq_ENCSR627NIF |
DNase-seq ENCSR627NIF [biosample_summary="Homo sapiens lung tissue male embryo (54 days) and male embryo (58 days)"]
|
 |
[6, 1.25e+04] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 33231519 | 1.03% | 221120 |
| chr1 | 2952991 | 1.19% | 19657 |
| chr2 | 2789467 | 1.15% | 18557 |
| chr3 | 2165421 | 1.09% | 14406 |
| chr4 | 1798961 | 0.95% | 11961 |
| chr5 | 1913044 | 1.05% | 12720 |
| chr6 | 2043043 | 1.20% | 13596 |
| chr7 | 1744291 | 1.09% | 11607 |
| chr8 | 1567220 | 1.08% | 10429 |
| chr9 | 1378976 | 1.00% | 9177 |
| chr10 | 1637378 | 1.22% | 10895 |
| chr11 | 1640356 | 1.21% | 10917 |
| chr12 | 1561511 | 1.17% | 10396 |
| chr13 | 984028 | 0.86% | 6553 |
| chr14 | 1051642 | 0.98% | 6993 |
| chr15 | 1069864 | 1.05% | 7123 |
| chr16 | 1025641 | 1.14% | 6829 |
| chr17 | 1314428 | 1.58% | 8745 |
| chr18 | 808163 | 1.01% | 5377 |
| chr19 | 915440 | 1.56% | 6098 |
| chr20 | 857142 | 1.33% | 5699 |
| chr21 | 383227 | 0.82% | 2550 |
| chr22 | 553569 | 1.09% | 3687 |
| chrX | 1017366 | 0.65% | 6762 |
| chrY | 58350 | 0.10% | 386 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 221120 | 8 | 450 | 150.29 | 150 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF811RTH.bed.gz | 2.11 MB | 1e2c734f52ad43c3fad65190a8f6a881 |
| ENCFF811RTH.tabix.bed.gz | 1.82 MB | abe009196835e81a6307b6a3f8f86438 |
| ENCFF811RTH.tabix.bed.gz.tbi | 699.02 KB | 29731ea6926e0225e1ad51a81b7183ab |
| genomic_resource.yaml | 3.09 KB | 10723142cb1841b320e8d72f4f886587 |
| statistics/ |