Resource
| Id | Histone_ChIP-seq/ENCSR643QXU |
|---|---|
| Type | position_score |
| Version | 0 |
| Summary | Histone_ChIP-seq ENCSR643QXU [biosample_summary="Homo sapiens SJSA1" and target="H3K36me3"] |
| Description |
status: released biological_replicates: Rep 1, Rep 2 summary: output_type: pseudoreplicated peaks audit_internal_action: Released analysis {ENCAN630CCB|/analyses/ENCAN630CCB/} has in progress subobject quality standard {encode4-histone-chip|/quality-standards/encode4-histone-chip/} 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 {ENCFF493XJW|/files/ENCFF493XJW/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC1 value of 0.84. 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 {ENCFF493XJW|/files/ENCFF493XJW/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 6.14. 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 {ENCFF397TKX|/files/ENCFF397TKX/} processed by ChIP-seq ENCODE4 v1.5.1 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 {ENCFF397TKX|/files/ENCFF397TKX/} processed by ChIP-seq ENCODE4 v1.5.1 GRCh38 pipeline was generated from a library with PBC2 value of 8.69. |
| Labels |
|
Scores (1)
| ID | Type | Default annotation | Description | Histogram | Range | Summary |
|---|---|---|---|---|---|---|
| Histone_ChIP-seq_ENCSR643QXU | float |
Histone_ChIP-seq_ENCSR643QXU |
Histone_ChIP-seq ENCSR643QXU [biosample_summary="Homo sapiens SJSA1" and target="H3K36me3"]
|
 |
[1.12, 23.4] |
|
n counts base pairs; sd is the population standard deviation.
Coverage
| Chromosome | Covered positions | Covered % | Segments |
|---|---|---|---|
| all chromosomes | 151605560 | 4.71% | 136700 |
| chr1 | 16256686 | 6.53% | 14028 |
| chr2 | 12450139 | 5.14% | 11378 |
| chr3 | 8615761 | 4.34% | 8938 |
| chr4 | 4702589 | 2.47% | 5047 |
| chr5 | 9353865 | 5.15% | 7936 |
| chr6 | 7389415 | 4.33% | 7218 |
| chr7 | 7300947 | 4.58% | 6942 |
| chr8 | 6277397 | 4.33% | 5828 |
| chr9 | 4997775 | 3.61% | 4858 |
| chr10 | 7148796 | 5.34% | 6597 |
| chr11 | 5879699 | 4.35% | 4772 |
| chr12 | 8531919 | 6.40% | 7539 |
| chr13 | 3215885 | 2.81% | 3409 |
| chr14 | 4538252 | 4.24% | 4557 |
| chr15 | 6153247 | 6.03% | 5522 |
| chr16 | 6651838 | 7.36% | 5329 |
| chr17 | 9508697 | 11.42% | 7547 |
| chr18 | 2832729 | 3.52% | 2767 |
| chr19 | 7786249 | 13.28% | 6103 |
| chr20 | 4420972 | 6.86% | 3680 |
| chr21 | 1972303 | 4.22% | 1615 |
| chr22 | 4134574 | 8.14% | 3134 |
| chrX | 1410834 | 0.90% | 1847 |
| chrY | 74992 | 0.13% | 109 |
| 3342 contigs with no values (129077085 bp) | 0 | 0.00% | 0 |
Segment lengths
| segments | min | max | mean | median | |
|---|---|---|---|---|---|
| segments | 136700 | 208 | 52910 | 1109.04 | 649 |
Files
| Filename | Size | md5 |
|---|---|---|
| ENCFF059FXY.bed.gz | 3.21 MB | 42bfb05a643d5e6934dd4098bd95877d |
| ENCFF059FXY.tabix.bed.gz | 1.41 MB | 54c29abf468852635f94da6d1cba0ab9 |
| ENCFF059FXY.tabix.bed.gz.tbi | 167.67 KB | 0a01731237fa654ab2147d8396b9aacd |
| genomic_resource.yaml | 4.0 KB | 52151621b732f4529b208a2fe9df806e |
| statistics/ |