Resource
| Id | Histone_ChIP-seq/ENCSR460SEN |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR460SEN [biosample_summary="Homo sapiens DOHH2" and target="H3K4me1"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN846CEQ|/analyses/ENCAN846CEQ/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} audit_internal_action: Released analysis {ENCAN846CEQ|/analyses/ENCAN846CEQ/} has in progress subobject document {909a6a9f-d1b5-4fb3-91ab-f3588a9e1566|/documents/909a6a9f-d1b5-4fb3-91ab-f3588a9e1566/} 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 {ENCFF732FGD|/files/ENCFF732FGD/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.82. 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 {ENCFF732FGD|/files/ENCFF732FGD/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 5.53. 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 {ENCFF090UDZ|/files/ENCFF090UDZ/} processed by ChIP-seq ENCODE4 v1.6.1 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 {ENCFF090UDZ|/files/ENCFF090UDZ/} processed by ChIP-seq ENCODE4 v1.6.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.92. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR460SEN | float |
Histone_ChIP-seq_ENCSR460SEN |
Histone_ChIP-seq ENCSR460SEN [biosample_summary="Homo sapiens DOHH2" and target="H3K4me1"]
|
 |
[1.53, 34.3] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 144880799 | 4.50% | 110705 |
| chr1 | 13012489 | 5.23% | 10236 |
| chr2 | 11804147 | 4.87% | 8880 |
| chr3 | 9831274 | 4.96% | 7368 |
| chr4 | 6255821 | 3.29% | 4909 |
| chr5 | 7150880 | 3.94% | 5567 |
| chr6 | 8683041 | 5.08% | 6746 |
| chr7 | 8031103 | 5.04% | 6056 |
| chr8 | 6525789 | 4.50% | 4722 |
| chr9 | 5795288 | 4.19% | 4282 |
| chr10 | 6870492 | 5.13% | 5063 |
| chr11 | 6841403 | 5.06% | 5159 |
| chr12 | 7949613 | 5.96% | 6179 |
| chr13 | 3560209 | 3.11% | 2653 |
| chr14 | 4980743 | 4.65% | 3798 |
| chr15 | 4687077 | 4.60% | 3571 |
| chr16 | 4997463 | 5.53% | 3858 |
| chr17 | 6745034 | 8.10% | 5272 |
| chr18 | 2836368 | 3.53% | 2152 |
| chr19 | 5523586 | 9.42% | 4598 |
| chr20 | 3972644 | 6.16% | 2897 |
| chr21 | 1408576 | 3.02% | 1080 |
| chr22 | 3818827 | 7.51% | 2617 |
| chrX | 3386868 | 2.17% | 2872 |
| chrY | 212064 | 0.37% | 170 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 110705 | 230 | 42872 | 1308.71 | 834 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF708CCJ.bed.gz | 2.83 MB | c31399eddd7ea94cbb3b06563aa6acad |
| ENCFF708CCJ.tabix.bed.gz | 1.2 MB | 858898134c5e95db18c292006a605227 |
| ENCFF708CCJ.tabix.bed.gz.tbi | 269.0 KB | 3346348873b550a125fedc12382e7b7d |
| genomic_resource.yaml | 4.22 KB | 827c09d061a8829a3269b864cafd835d |
| statistics/ |