Resource
| Id | Histone_ChIP-seq/ENCSR074TRC |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR074TRC [biosample_summary="Homo sapiens SK-N-SH" and target="H3K79me2"] |
| Description |
status: archived biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN155KKA|/analyses/ENCAN155KKA/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed alignments file {ENCFF921IYR|/files/ENCFF921IYR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 9276879 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 {ENCFF388DSF|/files/ENCFF388DSF/} processed by ChIP-seq ENCODE3 GRCh38 pipeline has 29211034 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 {ENCFF921IYR|/files/ENCFF921IYR/} 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 {ENCFF921IYR|/files/ENCFF921IYR/} processed by ChIP-seq ENCODE3 GRCh38 pipeline was generated from a library with PBC2 value of 8.99. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR074TRC | float |
Histone_ChIP-seq_ENCSR074TRC |
Histone_ChIP-seq ENCSR074TRC [biosample_summary="Homo sapiens SK-N-SH" and target="H3K79me2"]
|
 |
[1.65, 25.9] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 168996203 | 5.25% | 101096 |
| chr1 | 16265385 | 6.53% | 9484 |
| chr1_KI270706v1_random | 688 | 0.39% | 2 |
| chr2 | 13144275 | 5.43% | 7903 |
| chr3 | 12204544 | 6.15% | 7418 |
| chr4 | 7884128 | 4.14% | 4933 |
| chr5 | 9315629 | 5.13% | 5510 |
| chr6 | 8091007 | 4.74% | 5387 |
| chr7 | 10001678 | 6.28% | 5543 |
| chr8 | 6384476 | 4.40% | 3967 |
| chr9 | 7709598 | 5.57% | 4856 |
| chr9_KI270720v1_random | 5148 | 13.18% | 7 |
| chr10 | 8450223 | 6.32% | 5345 |
| chr11 | 8512008 | 6.30% | 4855 |
| chr12 | 8912406 | 6.69% | 5040 |
| chr13 | 4513443 | 3.95% | 2761 |
| chr14 | 5380678 | 5.03% | 3131 |
| chr14_GL000009v2_random | 6232 | 3.09% | 14 |
| chr14_GL000194v1_random | 13263 | 6.93% | 24 |
| chr14_GL000225v1_random | 290 | 0.14% | 1 |
| chr14_KI270722v1_random | 3491 | 1.80% | 5 |
| chr14_KI270726v1_random | 2904 | 6.64% | 5 |
| chr15 | 6762864 | 6.63% | 3990 |
| chr16 | 6041624 | 6.69% | 3511 |
| chr17 | 8718240 | 10.47% | 4733 |
| chr17_GL000205v2_random | 521 | 0.28% | 1 |
| chr18 | 3057697 | 3.80% | 1858 |
| chr19 | 5989503 | 10.22% | 3562 |
| chr20 | 4018773 | 6.24% | 2246 |
| chr21 | 1478258 | 3.16% | 919 |
| chr22 | 3162417 | 6.22% | 1918 |
| chrUn_GL000195v1 | 6439 | 3.52% | 6 |
| chrUn_GL000219v1 | 8920 | 4.98% | 6 |
| chrUn_KI270744v1 | 1258 | 0.75% | 4 |
| chrX | 2948195 | 1.89% | 2151 |
| 3332 contigs with no values (184532098 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 101096 | 195 | 104140 | 1671.64 | 734 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF703MCA.bed.gz | 2.43 MB | 8ef2f161c7473e7e79c61de624357f73 |
| ENCFF703MCA.tabix.bed.gz | 1.06 MB | 3528f0499286eee6ceadfa540b9143cb |
| ENCFF703MCA.tabix.bed.gz.tbi | 138.13 KB | 08afe696ecacfe69ceb8bcdeb6079a47 |
| genomic_resource.yaml | 3.68 KB | eaabf83a8f44a9b4747fe89532928ab9 |
| statistics/ |