Resource
| Id | Histone_ChIP-seq/ENCSR525XER |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR525XER [biosample_summary="Homo sapiens skeletal muscle satellite cell female adult originated from mesodermal cell" and target="H3K9me3"] |
| Description |
status: released biological_replicates: Rep 2, Rep 3 summary: female adult output_type: replicated peaks audit_internal_action: Archived analysis {ENCAN970CFH|/analyses/ENCAN970CFH/} has in progress subobject quality standard {encode3-histone-chip|/quality-standards/encode3-histone-chip/} audit_not_compliant: Processed redacted unfiltered alignments file {ENCFF613REE|/files/ENCFF613REE/} processed by ChIP-seq ENCODE3 hg19 pipeline has 28102220 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_not_compliant: Processed redacted unfiltered alignments file {ENCFF141RAM|/files/ENCFF141RAM/} processed by ChIP-seq ENCODE3 hg19 pipeline has 30858986 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 redacted alignments file {ENCFF260EXP|/files/ENCFF260EXP/} 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 redacted alignments file {ENCFF260EXP|/files/ENCFF260EXP/} processed by ChIP-seq ENCODE3 hg19 pipeline was generated from a library with PBC2 value of 8.79. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR525XER | float |
Histone_ChIP-seq_ENCSR525XER |
Histone_ChIP-seq ENCSR525XER [biosample_summary="Homo sapiens skeletal muscle satellite cell female adult originated from mesodermal cell" and target="H3K9me3"]
|
 |
[1.46, 12.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 32248778 | 1.00% | 81626 |
| chr1 | 1815891 | 0.73% | 4506 |
| chr2 | 2375539 | 0.98% | 6235 |
| chr3 | 1335123 | 0.67% | 3572 |
| chr4 | 1809947 | 0.95% | 4778 |
| chr5 | 2095922 | 1.15% | 5491 |
| chr6 | 1254723 | 0.73% | 3363 |
| chr7 | 1897086 | 1.19% | 4905 |
| chr8 | 2250015 | 1.55% | 5751 |
| chr9 | 679218 | 0.49% | 1745 |
| chr10 | 1935338 | 1.45% | 4791 |
| chr11 | 1197971 | 0.89% | 3182 |
| chr12 | 1251799 | 0.94% | 3031 |
| chr13 | 1226199 | 1.07% | 3318 |
| chr14 | 1445082 | 1.35% | 3813 |
| chr15 | 1021772 | 1.00% | 2505 |
| chr16 | 1305612 | 1.45% | 3350 |
| chr17 | 632694 | 0.76% | 1572 |
| chr18 | 1325989 | 1.65% | 3420 |
| chr19 | 1884583 | 3.22% | 3560 |
| chr20 | 656850 | 1.02% | 1606 |
| chr21 | 736486 | 1.58% | 1589 |
| chr22 | 759982 | 1.50% | 1703 |
| chrX | 1310100 | 0.84% | 3755 |
| chrY | 44857 | 0.08% | 85 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 81626 | 180 | 13086 | 395.08 | 337 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF089EQE.bed.gz | 1.31 MB | e02725c4d469de3388a9bb836c4fb529 |
| ENCFF089EQE.tabix.bed.gz | 720.48 KB | a7fe72ede48b2c1eb78d2932aa9ae830 |
| ENCFF089EQE.tabix.bed.gz.tbi | 230.97 KB | caf580844dab211dc7fddad1c03d824a |
| genomic_resource.yaml | 3.97 KB | f52f3596550c09c2e6ca1c1625aa95ad |
| statistics/ |