Resource
| Id | Histone_ChIP-seq/ENCSR958ZMM |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR958ZMM [biosample_summary="Homo sapiens neural cell originated from H1" and target="H4K20me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: male embryo output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN984HRJ|/analyses/ENCAN984HRJ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN984HRJ|/analyses/ENCAN984HRJ/} has in progress subobject document {ce9320b4-7c32-4e7f-bcd4-a8b9c81dba92|/documents/ce9320b4-7c32-4e7f-bcd4-a8b9c81dba92/} audit_not_compliant: Processed alignments file {ENCFF136JPJ|/files/ENCFF136JPJ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 31222385 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_not_compliant: Processed alignments file {ENCFF682KHR|/files/ENCFF682KHR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline has 23013539 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 {ENCFF682KHR|/files/ENCFF682KHR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.85. 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 {ENCFF682KHR|/files/ENCFF682KHR/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.67. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR958ZMM | float |
Histone_ChIP-seq_ENCSR958ZMM |
Histone_ChIP-seq ENCSR958ZMM [biosample_summary="Homo sapiens neural cell originated from H1" and target="H4K20me1"]
|
 |
[1.76, 13.6] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 5463819 | 0.17% | 7166 |
| chr1 | 616581 | 0.25% | 821 |
| chr2 | 415696 | 0.17% | 595 |
| chr3 | 227161 | 0.11% | 332 |
| chr4 | 165548 | 0.09% | 260 |
| chr5 | 518438 | 0.29% | 504 |
| chr6 | 179037 | 0.10% | 269 |
| chr7 | 316271 | 0.20% | 402 |
| chr8 | 163455 | 0.11% | 219 |
| chr9 | 169898 | 0.12% | 258 |
| chr10 | 214209 | 0.16% | 315 |
| chr11 | 235785 | 0.17% | 324 |
| chr12 | 157668 | 0.12% | 249 |
| chr13 | 37167 | 0.03% | 59 |
| chr14 | 207341 | 0.19% | 241 |
| chr15 | 236822 | 0.23% | 275 |
| chr16 | 385050 | 0.43% | 424 |
| chr17 | 417708 | 0.50% | 510 |
| chr18 | 110839 | 0.14% | 193 |
| chr19 | 279338 | 0.48% | 356 |
| chr20 | 197035 | 0.31% | 250 |
| chr21 | 29686 | 0.06% | 51 |
| chr22 | 172963 | 0.34% | 245 |
| chrX | 10123 | 0.01% | 14 |
| 3343 contigs with no values (186304500 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 7166 | 188 | 19278 | 762.46 | 534 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF609DIL.bed.gz | 150.96 KB | 9e8af02f5bcf7d7358ffc0783da94b03 |
| ENCFF609DIL.tabix.bed.gz | 74.63 KB | dd776d60e4105f25c9fdbd23dab5ce2e |
| ENCFF609DIL.tabix.bed.gz.tbi | 31.31 KB | 646f3d014654800b4a7b526a4be481ce |
| genomic_resource.yaml | 4.06 KB | 9f043cee8ba7ab91fe8b319eace27bad |
| statistics/ |