Resource
| Id | Histone_ChIP-seq/ENCSR426UWA |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR426UWA [biosample_summary="Homo sapiens HUES64" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN238FCR|/analyses/ENCAN238FCR/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF258TLW|/files/ENCFF258TLW/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 24520826 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_not_compliant: Processed alignments file {ENCFF602HGV|/files/ENCFF602HGV/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 28153066 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 alignments file {ENCFF258TLW|/files/ENCFF258TLW/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.88. 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 alignments file {ENCFF258TLW|/files/ENCFF258TLW/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.26. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR426UWA | float |
Histone_ChIP-seq_ENCSR426UWA |
Histone_ChIP-seq ENCSR426UWA [biosample_summary="Homo sapiens HUES64" and target="H3K36me3"]
|
 |
[1.23, 39.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 168643082 | 5.24% | 151905 |
| chr1 | 16737688 | 6.72% | 14526 |
| chr2 | 13385232 | 5.53% | 11616 |
| chr3 | 10672623 | 5.38% | 9528 |
| chr4 | 7889968 | 4.15% | 6951 |
| chr5 | 9670347 | 5.33% | 8193 |
| chr6 | 8199884 | 4.80% | 7229 |
| chr7 | 8054770 | 5.05% | 7716 |
| chr8 | 6487671 | 4.47% | 5768 |
| chr9 | 6981269 | 5.04% | 6241 |
| chr10 | 7058868 | 5.28% | 6387 |
| chr11 | 8119849 | 6.01% | 7064 |
| chr12 | 9404089 | 7.06% | 8343 |
| chr13 | 4010262 | 3.51% | 3732 |
| chr14 | 5782289 | 5.40% | 5167 |
| chr15 | 6039936 | 5.92% | 5496 |
| chr16 | 6117400 | 6.77% | 5531 |
| chr17 | 8106936 | 9.74% | 7531 |
| chr17_GL000205v2_random | 935 | 0.50% | 1 |
| chr18 | 3336056 | 4.15% | 3001 |
| chr19 | 7948165 | 13.56% | 7959 |
| chr20 | 4484102 | 6.96% | 3938 |
| chr21 | 1932208 | 4.14% | 1638 |
| chr22 | 3536720 | 6.96% | 3346 |
| chrUn_GL000195v1 | 3823 | 2.09% | 7 |
| chrUn_KI270467v1 | 247 | 6.30% | 1 |
| chrX | 4320542 | 2.77% | 4599 |
| chrY | 361203 | 0.63% | 396 |
| 3339 contigs with no values (128704678 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 151905 | 170 | 50985 | 1110.19 | 650 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF041EXV.bed.gz | 3.31 MB | 3271f24a26bb63eabba46ed4fd2ad059 |
| ENCFF041EXV.tabix.bed.gz | 1.52 MB | cf56a90301a6d3ce570b8c28ebb1e49d |
| ENCFF041EXV.tabix.bed.gz.tbi | 171.59 KB | 817980b31645b120a21f0b1810437b4d |
| genomic_resource.yaml | 3.68 KB | 2a534190c2374b03bfe85dfa10e68327 |
| statistics/ |