public final class RrbsSummaryMetrics extends MultilevelMetrics
Modifier and Type | Field and 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_SEEN / CPG_BASES_CONVERTED
|
Double |
PCT_NON_CPG_BASES_CONVERTED
NON_CPG_BASES / NON_CPG_CONVERTED_BASES
|
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 and 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