Resource
| Id | Histone_ChIP-seq/ENCSR000DXB |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR000DXB [biosample_summary="Homo sapiens Panc1" and target="H3K4me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN566IIP|/analyses/ENCAN566IIP/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed alignments file {ENCFF879LKK|/files/ENCFF879LKK/} processed by ChIP-seq ENCODE3 hg19 pipeline has 16185677 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 million is acceptable. (See {ENCODE ChIP-seq data standards|/data-standards/chip-seq/}) audit_warning: Processed alignments file {ENCFF859UMC|/files/ENCFF859UMC/} processed by ChIP-seq ENCODE3 hg19 pipeline has 15598483 usable fragments. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K4me3-human and investigated as a narrow histone mark is 10 million usable fragments. The recommended value is > 20 million, but > 10 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 {ENCFF879LKK|/files/ENCFF879LKK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC1 value of 0.87. 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 {ENCFF879LKK|/files/ENCFF879LKK/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.65. 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 {ENCFF859UMC|/files/ENCFF859UMC/} processed by ChIP-seq ENCODE3 hg19 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 {ENCFF859UMC|/files/ENCFF859UMC/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.86. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR000DXB | float |
Histone_ChIP-seq_ENCSR000DXB |
Histone_ChIP-seq ENCSR000DXB [biosample_summary="Homo sapiens Panc1" and target="H3K4me3"]
|
 |
[1.74, 132] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 44945763 | 1.40% | 37138 |
| chr1 | 4385941 | 1.76% | 3515 |
| chr2 | 3144630 | 1.30% | 2662 |
| chr3 | 2405360 | 1.21% | 1960 |
| chr4 | 1650943 | 0.87% | 1446 |
| chr5 | 2251892 | 1.24% | 1822 |
| chr6 | 2871508 | 1.68% | 2201 |
| chr7 | 2312570 | 1.45% | 1981 |
| chr8 | 1541569 | 1.06% | 1366 |
| chr9 | 1659971 | 1.20% | 1447 |
| chr10 | 2058050 | 1.54% | 1714 |
| chr11 | 2504323 | 1.85% | 1923 |
| chr12 | 2395872 | 1.80% | 1846 |
| chr13 | 913198 | 0.80% | 841 |
| chr14 | 1326818 | 1.24% | 1071 |
| chr15 | 1479315 | 1.45% | 1192 |
| chr16 | 1790744 | 1.98% | 1551 |
| chr17 | 2668342 | 3.20% | 2105 |
| chr18 | 764926 | 0.95% | 730 |
| chr19 | 2791337 | 4.76% | 2340 |
| chr20 | 1257013 | 1.95% | 1059 |
| chr21 | 449743 | 0.96% | 424 |
| chr22 | 934818 | 1.84% | 830 |
| chrX | 1385252 | 0.89% | 1108 |
| chrY | 1628 | <0.01% | 4 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 37138 | 185 | 39528 | 1210.24 | 836.5 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF344GEX.bed.gz | 950.63 KB | 856853e182bd597ec5996ca9a80a1c38 |
| ENCFF344GEX.tabix.bed.gz | 415.22 KB | cc450698aad3a95ee1d2a9f5de2f82d8 |
| ENCFF344GEX.tabix.bed.gz.tbi | 182.12 KB | 7239a5c1f19331d573444868cd24459d |
| genomic_resource.yaml | 5.25 KB | c5b3ca5b9e26086623e87a3924d2979c |
| statistics/ |