Resource
| Id | Histone_ChIP-seq/ENCSR605SXJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR605SXJ [biosample_summary="Homo sapiens naive thymus-derived CD4-positive, alpha-beta T cell" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN787HHE|/analyses/ENCAN787HHE/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted alignments file {ENCFF324OZH|/files/ENCFF324OZH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 17984657 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K36me3-human and investigated as a broad histone mark is 20 million usable fragments. The recommended value is > 45 million, but > 35 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) 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 > 0.8 is acceptable. ENCODE processed redacted alignments file {ENCFF324OZH|/files/ENCFF324OZH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.90. audit_warning: PBC2 (PCR Bottlenecking Coefficient 2, M1/M2) is the ratio of the number of genomic locations where exactly one read maps uniquely (M1) to the number of genomic locations where two reads map uniquely (M2). A PBC2 value in the range 0 - 1 is severe bottlenecking, 1 - 3 is moderate bottlenecking, 3 - 10 is mild bottlenecking, > 10 is no bottlenecking. PBC2 value > 10 is recommended, but > 3 is acceptable. ENCODE processed redacted alignments file {ENCFF324OZH|/files/ENCFF324OZH/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.77. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR605SXJ | float |
Histone_ChIP-seq_ENCSR605SXJ |
Histone_ChIP-seq ENCSR605SXJ [biosample_summary="Homo sapiens naive thymus-derived CD4-positive, alpha-beta T cell" and target="H3K36me3"]
|
 |
[1.89, 12.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 21070401 | 0.65% | 34799 |
| chr1 | 2183717 | 0.88% | 3508 |
| chr2 | 1650708 | 0.68% | 2812 |
| chr3 | 1224324 | 0.62% | 2103 |
| chr4 | 629944 | 0.33% | 1125 |
| chr5 | 1132358 | 0.62% | 1818 |
| chr6 | 892117 | 0.52% | 1512 |
| chr7 | 822218 | 0.52% | 1425 |
| chr8 | 607750 | 0.42% | 1053 |
| chr9 | 917905 | 0.66% | 1464 |
| chr10 | 791327 | 0.59% | 1372 |
| chr11 | 1182289 | 0.88% | 1868 |
| chr12 | 1245581 | 0.93% | 2016 |
| chr13 | 398968 | 0.35% | 691 |
| chr14 | 777594 | 0.73% | 1274 |
| chr15 | 699045 | 0.69% | 1175 |
| chr16 | 1008868 | 1.12% | 1626 |
| chr17 | 1356137 | 1.63% | 2221 |
| chr18 | 277950 | 0.35% | 496 |
| chr19 | 1435701 | 2.45% | 2166 |
| chr20 | 661293 | 1.03% | 1073 |
| chr21 | 271778 | 0.58% | 447 |
| chr22 | 651021 | 1.28% | 1028 |
| chrX | 239638 | 0.15% | 494 |
| chrY | 12170 | 0.02% | 32 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 34799 | 220 | 5337 | 605.49 | 509 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF988ZPL.bed.gz | 680.42 KB | 378db2667baa6af6606623dba644bb17 |
| ENCFF988ZPL.tabix.bed.gz | 346.44 KB | 288454883e4b1942e7ce52bb3dd264a5 |
| ENCFF988ZPL.tabix.bed.gz.tbi | 113.87 KB | 33aab068e2a79e6a03dbea604b8d4090 |
| genomic_resource.yaml | 3.35 KB | fb2b7c6b178e4c826940062ef6702774 |
| statistics/ |