Resource
| Id | Histone_ChIP-seq/ENCSR154HDX |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR154HDX [biosample_summary="Homo sapiens GM23338 originated from GM23248" and target="H3K79me2"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN593YSD|/analyses/ENCAN593YSD/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF263XBT|/files/ENCFF263XBT/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 20968563 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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 {ENCFF531WSU|/files/ENCFF531WSU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 19646428 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K79me2-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 {ENCFF531WSU|/files/ENCFF531WSU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC1 value of 0.89. 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 {ENCFF531WSU|/files/ENCFF531WSU/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 9.12. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR154HDX | float |
Histone_ChIP-seq_ENCSR154HDX |
Histone_ChIP-seq ENCSR154HDX [biosample_summary="Homo sapiens GM23338 originated from GM23248" and target="H3K79me2"]
|
 |
[1.4, 56.1] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 151138143 | 4.70% | 81015 |
| chr1 | 14439348 | 5.80% | 7430 |
| chr2 | 12316213 | 5.09% | 5885 |
| chr3 | 9858426 | 4.97% | 5459 |
| chr4 | 7265757 | 3.82% | 4049 |
| chr5 | 7921422 | 4.36% | 4228 |
| chr6 | 8767600 | 5.13% | 4859 |
| chr7 | 9006962 | 5.65% | 5064 |
| chr8 | 6849884 | 4.72% | 3551 |
| chr9 | 6658288 | 4.81% | 3930 |
| chr10 | 7027690 | 5.25% | 3750 |
| chr11 | 6595813 | 4.88% | 3659 |
| chr12 | 7546926 | 5.66% | 4042 |
| chr13 | 3884280 | 3.40% | 2179 |
| chr14 | 4934264 | 4.61% | 2620 |
| chr15 | 5187438 | 5.09% | 2676 |
| chr16 | 5101964 | 5.65% | 2829 |
| chr17 | 6364239 | 7.64% | 3422 |
| chr17_GL000205v2_random | 2770 | 1.49% | 3 |
| chr18 | 2953032 | 3.67% | 1521 |
| chr19 | 5270593 | 8.99% | 2923 |
| chr20 | 3561779 | 5.53% | 1769 |
| chr21 | 1510195 | 3.23% | 677 |
| chr22 | 3424425 | 6.74% | 1643 |
| chr22_KI270733v1_random | 346 | 0.19% | 1 |
| chrUn_GL000195v1 | 9831 | 5.38% | 8 |
| chrUn_GL000218v1 | 332 | 0.21% | 1 |
| chrX | 4263843 | 2.73% | 2602 |
| chrY | 414483 | 0.72% | 235 |
| 3338 contigs with no values (128367679 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 81015 | 195 | 166396 | 1865.56 | 771 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF687IIW.bed.gz | 1.89 MB | bf73fcabea1335b3b5b460cc7ada20d7 |
| ENCFF687IIW.tabix.bed.gz | 860.96 KB | 4590f0a6ee3338922f6ece4c0b9a4015 |
| ENCFF687IIW.tabix.bed.gz.tbi | 134.35 KB | 0250b801dc579c8c508a427705dcb22d |
| genomic_resource.yaml | 3.75 KB | dd0d7afba084d1f71e8bcf2926803878 |
| statistics/ |