Resource
| Id | DNase-seq/ENCSR339TVH |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | DNase-seq ENCSR339TVH [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (90 or above years) with mild cognitive impairment output_type: peaks 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 {ENCFF948ZYY|/files/ENCFF948ZYY/} 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_ENCSR339TVH | float |
DNase-seq_ENCSR339TVH |
DNase-seq ENCSR339TVH [biosample_summary="Homo sapiens with mild cognitive impairment; head of caudate nucleus tissue female adult (90 or above years)"]
|
 |
[0.145, 20.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9119070 | 0.28% | 51287 |
| chr1 | 906946 | 0.36% | 5085 |
| chr2 | 653515 | 0.27% | 3734 |
| chr3 | 542726 | 0.27% | 3050 |
| chr4 | 368037 | 0.19% | 2098 |
| chr5 | 452296 | 0.25% | 2578 |
| chr6 | 491976 | 0.29% | 2769 |
| chr7 | 441516 | 0.28% | 2534 |
| chr8 | 372879 | 0.26% | 2141 |
| chr9 | 407554 | 0.29% | 2291 |
| chr10 | 411771 | 0.31% | 2335 |
| chr11 | 510738 | 0.38% | 2890 |
| chr12 | 466215 | 0.35% | 2625 |
| chr13 | 194901 | 0.17% | 1097 |
| chr14 | 294350 | 0.27% | 1658 |
| chr15 | 294489 | 0.29% | 1659 |
| chr16 | 366166 | 0.41% | 2048 |
| chr17 | 482295 | 0.58% | 2664 |
| chr18 | 165393 | 0.21% | 974 |
| chr19 | 521397 | 0.89% | 2737 |
| chr20 | 249069 | 0.39% | 1405 |
| chr21 | 92721 | 0.20% | 524 |
| chr22 | 208805 | 0.41% | 1171 |
| chrX | 223081 | 0.14% | 1218 |
| chrY | 234 | <0.01% | 2 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 51287 | 6 | 800 | 177.8 | 178 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF126LDW.bed.gz | 562.11 KB | 4fc120db2b9a026df2be4724fbcfbda4 |
| ENCFF126LDW.tabix.bed.gz | 509.71 KB | 4ac6acc245a6dd74776dba38686326c0 |
| ENCFF126LDW.tabix.bed.gz.tbi | 265.31 KB | 74242f2bbf170875c7e500fd5b647d50 |
| genomic_resource.yaml | 2.29 KB | ec29c7ed5c22ade44d63530333685c98 |
| statistics/ |