Resource
| Id | Histone_ChIP-seq/ENCSR394DRL |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR394DRL [biosample_summary="Homo sapiens psoas muscle tissue male child (3 years)" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 1 summary: male child (3 years) output_type: pseudoreplicated peaks audit_internal_action: Archived analysis {ENCAN648ISC|/analyses/ENCAN648ISC/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_warning: Processed unfiltered alignments file {ENCFF085TDZ|/files/ENCFF085TDZ/} processed by ChIP-seq ENCODE3 hg19 pipeline has 37889988 mapped reads. The minimum ENCODE standard for each replicate in a ChIP-seq experiment targeting H3K9me3-human and investigated as a broad histone mark is 35 million mapped reads. 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 {ENCFF515BMO|/files/ENCFF515BMO/} 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 {ENCFF515BMO|/files/ENCFF515BMO/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 9.13. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR394DRL | float |
Histone_ChIP-seq_ENCSR394DRL |
Histone_ChIP-seq ENCSR394DRL [biosample_summary="Homo sapiens psoas muscle tissue male child (3 years)" and target="H3K9me3"]
|
 |
[1.74, 11.8] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 9813963 | 0.31% | 27032 |
| chr1 | 596967 | 0.24% | 1688 |
| chr2 | 702789 | 0.29% | 2088 |
| chr3 | 583743 | 0.29% | 1674 |
| chr4 | 662299 | 0.35% | 1946 |
| chr5 | 721898 | 0.40% | 2058 |
| chr6 | 524197 | 0.31% | 1560 |
| chr7 | 547398 | 0.34% | 1546 |
| chr8 | 575169 | 0.40% | 1656 |
| chr9 | 383449 | 0.28% | 1032 |
| chr10 | 473340 | 0.35% | 1332 |
| chr11 | 398499 | 0.29% | 1174 |
| chr12 | 520787 | 0.39% | 1388 |
| chr13 | 285664 | 0.25% | 878 |
| chr14 | 273759 | 0.26% | 795 |
| chr15 | 248260 | 0.24% | 684 |
| chr16 | 372710 | 0.41% | 954 |
| chr17 | 145213 | 0.17% | 400 |
| chr18 | 261259 | 0.33% | 788 |
| chr19 | 1076352 | 1.84% | 2126 |
| chr20 | 183773 | 0.29% | 517 |
| chr21 | 166664 | 0.36% | 438 |
| chr22 | 52487 | 0.10% | 150 |
| chrM | 7022 | 42.38% | 13 |
| chrX | 35531 | 0.02% | 107 |
| chrY | 14734 | 0.03% | 40 |
| 3341 contigs with no values (129060516 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 27032 | 150 | 5863 | 363.05 | 310 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF402CHB.bed.gz | 473.15 KB | 3a78e63e504c4669d783c88568b2bf86 |
| ENCFF402CHB.tabix.bed.gz | 246.82 KB | 7b2c4b42de77894fe6adc948978457e5 |
| ENCFF402CHB.tabix.bed.gz.tbi | 167.25 KB | d6c0e51ab6b541db40e9eefd10d3e205 |
| genomic_resource.yaml | 3.22 KB | ca06fb05226195beb2371511090d4b89 |
| statistics/ |