RNA-seq Metrics

Read Count Metrics

The following summary statistics are calculated by counting the number of reads that have the given characteristics.

Total Reads

Total Purity Filtered Reads Sequenced are filtered for vendor fail flags and exclude alternative alignment reads. Alternative Aligments are duplicate read entries providing alternative coordinates. Failed Vendor QC Check are reads which have been designated as failed by the sequencer. Read Length is the maximum length found for all reads. Estimated Library Size is the number of expected fragments based upon the total number of reads and duplication rate assuming a Poisson distribution.

Mapped Reads

Mapped reads are those that were aligned. Mapping Rate is per total reads. Mapped Unique are both aligned as well as non-duplicate reads. Mapped Unique Rate of Total is per total reads. Unique Rate of Mapped are unique reads divided by all mapped reads. Duplication Rate of Mapped is the duplicate read divided by total mapped reads. Base Mismatch Rate is the number of bases not matching the reference divided by the total number of aligned bases. rRNA reads are non-duplicate and duplicate reads aligning to rRNA regions as defined in the transcript model definition. rRNA Rate is per total reads.

Mate Pairs

Mapped Pairs is the total number of pairs for which both ends map. Unpaired Reads are the number of reads that are lacking a mate. End 1/2 Mapping Rate is the number of mapped divided by the total number of End1/End2 reads. End 1/2 Mismatch Rate is the number of End 1 and 2 bases not matching the reference divided by the total number of mapped End 1 and 2 bases. Fragment Length Mean/StdDev is the mean distance, standard deviation between the start of an upstream read and the end of the downstream one. Only fragments contained within single exons are used. Chimeric Pairs are pairs whose mates map to different genes.

Transcript-associated Reads

All of the above rates are per mapped read. Intragenic Rate refers to the fraction of reads that map within genes (within introns or exons). Exonic Rate is the fraction mapping within exons. Intronic Rate is the fraction mapping within introns. Intergenic Rate is the fraction mapping in the genomic space between genes. Split Reads is the number of reads spanning an exon exon junction. Expression Profile Efficiency is the ratio of exon reads to total reads. Transcripts/Genes Detected is the number of transcripts/Genes with at least 5 reads.

Strand Specificity

End 1/2 Sense are the number of End 1 or 2 reads that were sequenced in the sense direction. Similarly, End 1/2 Antisense are the number of End 1 or 2 reads that were sequenced in the antisense direction.End 1/2 Sense % are percentages of intragenic End 1/2 reads that were sequenced in the sense direction.

Coverage Metrics for Bottom 1000 Expressed Transcripts

The metrics in this table are calculated across the transcripts that were determined to have the highest expression levels.

Sample	Note	Mean Per Base Cov.	Mean CV	No. Covered 5'	5'200Base Norm	No. Covered 3'	3' 200Base Norm	Num. Gaps	Cumul. Gap Length	Gap %
ExpoNoTrim	ExpoNoTrim	0.48	1.69	173	0.37	143	0.452	11247	1452918	67.9

It is important to note that these values are restricted to the bottom 1000 expressed transcripts. 5' and 3' values are per-base coverage averaged across all top transcripts. 5' and 3' ends are 200 base pairs. Gap % is the total cumulative gap length divided by the total cumulative transcript lengths.

Coverage Metrics for Middle 1000 Expressed Transcripts

The metrics in this table are calculated across the transcripts that were determined to have the highest expression levels.

Sample	Note	Mean Per Base Cov.	Mean CV	No. Covered 5'	5'200Base Norm	No. Covered 3'	3' 200Base Norm	Num. Gaps	Cumul. Gap Length	Gap %
ExpoNoTrim	ExpoNoTrim	1.49	1.06	450	0.36	422	0.432	12174	690672	33.8

It is important to note that these values are restricted to the middle 1000 expressed transcripts. 5' and 3' values are per-base coverage averaged across all top transcripts. 5' and 3' ends are 200 base pairs. Gap % is the total cumulative gap length divided by the total cumulative transcript lengths.

Coverage Metrics for Top 1000 Expressed Transcripts

The metrics in this table are calculated across the transcripts that were determined to have the highest expression levels.

Sample	Note	Mean Per Base Cov.	Mean CV	No. Covered 5'	5'200Base Norm	No. Covered 3'	3' 200Base Norm	Num. Gaps	Cumul. Gap Length	Gap %
ExpoNoTrim	ExpoNoTrim	429.50	0.79	857	0.25	894	0.424	1182	78893	12.0

It is important to note that these values are restricted to the top 1000 expressed transcripts. 5' and 3' values are per-base coverage averaged across all top transcripts. 5' and 3' ends are 200 base pairs. Gap % is the total cumulative gap length divided by the total cumulative transcript lengths.

Mean Coverage

Low Expressed

Medium Expressed

High Expressed

Mean Coverage from 3' End

Low Expressed

Medium Expressed

High Expressed

Files

Summary of Runtime Parameters

Generated by RNA-SeQC v1.1.8.1 07/11/14

Run on Thu Jun 04 20:58:22 PDT 2015