Resource
| Id | Histone_ChIP-seq/ENCSR159CDJ |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR159CDJ [biosample_summary="Homo sapiens Karpas-422" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN728FKO|/analyses/ENCAN728FKO/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN728FKO|/analyses/ENCAN728FKO/} has in progress subobject document {bad21172-6255-4d77-92ed-939ef1aac641|/documents/bad21172-6255-4d77-92ed-939ef1aac641/} audit_not_compliant: Processed alignments file {ENCFF623AYS|/files/ENCFF623AYS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 22978711 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-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: Processed alignments file {ENCFF935TGI|/files/ENCFF935TGI/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 35956124 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H4K20me1-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 {ENCFF623AYS|/files/ENCFF623AYS/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF623AYS|/files/ENCFF623AYS/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.46. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR159CDJ | float |
Histone_ChIP-seq_ENCSR159CDJ |
Histone_ChIP-seq ENCSR159CDJ [biosample_summary="Homo sapiens Karpas-422" and target="H4K20me1"]
|
 |
[1.58, 11.2] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 29718599 | 0.92% | 38614 |
| chr1 | 2549855 | 1.02% | 3344 |
| chr2 | 2357995 | 0.97% | 3004 |
| chr3 | 1796097 | 0.91% | 2337 |
| chr4 | 1020691 | 0.54% | 1283 |
| chr5 | 1327485 | 0.73% | 1767 |
| chr6 | 1621422 | 0.95% | 2088 |
| chr7 | 1469284 | 0.92% | 1969 |
| chr8 | 1275704 | 0.88% | 1729 |
| chr9 | 1336352 | 0.97% | 1744 |
| chr10 | 1376075 | 1.03% | 1745 |
| chr11 | 1288019 | 0.95% | 1699 |
| chr12 | 1179094 | 0.88% | 1542 |
| chr13 | 719665 | 0.63% | 933 |
| chr14 | 1531985 | 1.43% | 1852 |
| chr15 | 831924 | 0.82% | 1116 |
| chr16 | 1398755 | 1.55% | 1790 |
| chr17 | 1510423 | 1.81% | 2054 |
| chr18 | 651084 | 0.81% | 847 |
| chr19 | 1629169 | 2.78% | 1936 |
| chr20 | 1064492 | 1.65% | 1353 |
| chr21 | 335339 | 0.72% | 502 |
| chr22 | 1031223 | 2.03% | 1423 |
| chrX | 416467 | 0.27% | 557 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 38614 | 200 | 14201 | 769.63 | 579 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF434NDO.bed.gz | 833.16 KB | 620534fa1d0b0c2088efa1b5b8a43a1e |
| ENCFF434NDO.tabix.bed.gz | 398.61 KB | 3d8f3e5b3a947f9a489235939b0519f1 |
| ENCFF434NDO.tabix.bed.gz.tbi | 105.78 KB | 36441c60fe0d33be27f1fe0b58e2e421 |
| genomic_resource.yaml | 3.94 KB | e1542563ffa75cfcc198c6e5b295014e |
| statistics/ |