public final class RrbsSummaryMetrics extends MultilevelMetrics
Modifier and Type | Field | Description |
---|---|---|
Integer |
CPG_BASES_CONVERTED |
Number of CpG sites that were converted (TG for +, CA for -)
|
Integer |
CPG_BASES_SEEN |
Number of CpG sites encountered
|
Double |
MEAN_CPG_COVERAGE |
Mean coverage of CpG sites
|
Integer |
MEDIAN_CPG_COVERAGE |
Median coverage of CpG sites
|
Integer |
NON_CPG_BASES |
Number of times a non-CpG cytosine was encountered
|
Integer |
NON_CPG_CONVERTED_BASES |
Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
|
Double |
PCT_CPG_BASES_CONVERTED |
CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
|
Double |
PCT_NON_CPG_BASES_CONVERTED |
NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
|
Integer |
READS_ALIGNED |
Number of mapped reads processed
|
Integer |
READS_IGNORED_MISMATCHES |
Number of reads discarded for exceeding the mismatch threshold
|
Integer |
READS_IGNORED_SHORT |
Number of reads discarded due to being too short
|
Integer |
READS_WITH_NO_CPG |
Number of reads discarded for having no CpG sites
|
LIBRARY, READ_GROUP, SAMPLE
Constructor | Description |
---|---|
RrbsSummaryMetrics() |
public Integer READS_ALIGNED
public Integer NON_CPG_BASES
public Integer NON_CPG_CONVERTED_BASES
public Double PCT_NON_CPG_BASES_CONVERTED
public Integer CPG_BASES_SEEN
public Integer CPG_BASES_CONVERTED
public Double PCT_CPG_BASES_CONVERTED
public Double MEAN_CPG_COVERAGE
public Integer MEDIAN_CPG_COVERAGE
public Integer READS_WITH_NO_CPG
public Integer READS_IGNORED_SHORT
public Integer READS_IGNORED_MISMATCHES