Resource
| Id | ATAC-seq/ENCSR201FIW |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR201FIW [biosample_summary="Homo sapiens thyroid gland tissue female adult (51 years)"] |
| Description |
status: released biological_replicates: Rep 1 summary: female adult (51 years) output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN189DMM|/analyses/ENCAN189DMM/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_internal_action: Released analysis {ENCAN189DMM|/analyses/ENCAN189DMM/} has in progress subobject document {c45b5f87-73ed-4360-9b51-f2aa82fc51ae|/documents/c45b5f87-73ed-4360-9b51-f2aa82fc51ae/} audit_warning: Alignment file {ENCFF983POL|/files/ENCFF983POL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 22406224 usable fragments. According to ENCODE4 standards, ATAC-seq assays processed by the uniform processing pipeline should have > 25 million usable fragments. 20-25 million is acceptable and < 15 million is not compliant. audit_warning: NRF (Non Redundant Fraction) is equal to the result of the division of the number of reads after duplicates removal by the total number of reads. An NRF value < 0.7 is poor complexity, between 0.7 and 0.9 is moderate complexity, and >= 0.9 high complexity. NRF value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF983POL|/files/ENCFF983POL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.816357. audit_warning: PBC1 (PCR Bottlenecking Coefficient 1, M1/M_distinct) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where some reads map (M_distinct). A PBC1 value in the range 0 - 0.5 is severe bottlenecking, 0.5 - 0.8 is moderate bottlenecking, 0.8 - 0.9 is mild bottlenecking, and > 0.9 is no bottlenecking. PBC1 value > 0.9 is recommended, but > 0.7 is acceptable. ENCODE processed file {ENCFF983POL|/files/ENCFF983POL/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.84. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR201FIW | float |
ATAC-seq_ENCSR201FIW |
ATAC-seq ENCSR201FIW [biosample_summary="Homo sapiens thyroid gland tissue female adult (51 years)"]
|
 |
[1.39, 34.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 45503826 | 1.41% | 92191 |
| chr1 | 4203549 | 1.69% | 8296 |
| chr2 | 3623568 | 1.50% | 7471 |
| chr3 | 2959938 | 1.49% | 6159 |
| chr4 | 2242338 | 1.18% | 4746 |
| chr5 | 2428679 | 1.34% | 5084 |
| chr6 | 2686523 | 1.57% | 5504 |
| chr7 | 2340071 | 1.47% | 4859 |
| chr8 | 2117250 | 1.46% | 4387 |
| chr9 | 2094249 | 1.51% | 4172 |
| chr10 | 2257619 | 1.69% | 4631 |
| chr11 | 2369945 | 1.75% | 4708 |
| chr12 | 2185946 | 1.64% | 4406 |
| chr13 | 1172929 | 1.03% | 2496 |
| chr14 | 1489791 | 1.39% | 2971 |
| chr15 | 1453512 | 1.43% | 2888 |
| chr16 | 1578380 | 1.75% | 3049 |
| chr17 | 1865007 | 2.24% | 3561 |
| chr18 | 1060537 | 1.32% | 2263 |
| chr19 | 1481078 | 2.53% | 2641 |
| chr20 | 1211268 | 1.88% | 2447 |
| chr21 | 526334 | 1.13% | 1070 |
| chr22 | 866237 | 1.70% | 1711 |
| chrX | 1287074 | 0.82% | 2663 |
| chrY | 2004 | <0.01% | 8 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 92191 | 150 | 2482 | 493.58 | 397 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF911HZG.bed.gz | 3.28 MB | afb9c47d9597a6c14d02d1ab865ee1e3 |
| ENCFF911HZG.tabix.bed.gz | 1015.27 KB | f40096abc340fe502dfd963c008d4658 |
| ENCFF911HZG.tabix.bed.gz.tbi | 437.84 KB | eb2321b5ea44edebc2481f723b04a647 |
| genomic_resource.yaml | 3.16 KB | 842c50a87601d8bbdb7d7ec305b50349 |
| statistics/ |