Resource
| Id | ATAC-seq/ENCSR335JVB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | ATAC-seq ENCSR335JVB [biosample_summary="Homo sapiens GM19372"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN538AQP|/analyses/ENCAN538AQP/} has in progress subobject quality standard {encode4-atac-seq|/quality-standards/encode4-atac-seq/} audit_warning: Alignment file {ENCFF301DFZ|/files/ENCFF301DFZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline has 24491676 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 {ENCFF301DFZ|/files/ENCFF301DFZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with NRF value of 0.857335. 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 {ENCFF301DFZ|/files/ENCFF301DFZ/} processed by ATAC-seq ENCODE4 v1.9.1 GRCh38 pipeline was generated from a library with a PBC1 value of 0.88. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| ATAC-seq_ENCSR335JVB | float |
ATAC-seq_ENCSR335JVB |
ATAC-seq ENCSR335JVB [biosample_summary="Homo sapiens GM19372"]
|
 |
[1.58, 40.5] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 46648756 | 1.45% | 84125 |
| chr1 | 4168355 | 1.67% | 7397 |
| chr2 | 4058432 | 1.68% | 7463 |
| chr3 | 3291960 | 1.66% | 6098 |
| chr4 | 2703432 | 1.42% | 5095 |
| chr5 | 2909169 | 1.60% | 5391 |
| chr6 | 3120444 | 1.83% | 5716 |
| chr7 | 2600426 | 1.63% | 4786 |
| chr8 | 2378620 | 1.64% | 4409 |
| chr9 | 1863082 | 1.35% | 3371 |
| chr10 | 2276544 | 1.70% | 4163 |
| chr11 | 2238745 | 1.66% | 3986 |
| chr12 | 2371357 | 1.78% | 4183 |
| chr13 | 1324383 | 1.16% | 2421 |
| chr14 | 1340610 | 1.25% | 2377 |
| chr15 | 1294200 | 1.27% | 2328 |
| chr16 | 1285693 | 1.42% | 2152 |
| chr17 | 1484994 | 1.78% | 2465 |
| chr18 | 1112856 | 1.38% | 2084 |
| chr19 | 1221884 | 2.08% | 1878 |
| chr20 | 986126 | 1.53% | 1783 |
| chr21 | 476968 | 1.02% | 837 |
| chr22 | 553968 | 1.09% | 896 |
| chrX | 1478091 | 0.95% | 2632 |
| chrY | 108417 | 0.19% | 214 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 84125 | 150 | 2927 | 554.52 | 466 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF546KKI.bed.gz | 3.32 MB | e609decc41c465b9c8d6a3b1bb7f9471 |
| ENCFF546KKI.tabix.bed.gz | 949.56 KB | deb8f3a7b498d45f25f69fb0cb384c0f |
| ENCFF546KKI.tabix.bed.gz.tbi | 398.06 KB | 35ea500677e57880315a0c78dbf5ec4b |
| genomic_resource.yaml | 2.86 KB | 0dd52208d453df627f7b2651c65432c5 |
| statistics/ |