Input data and parameters 

Input

Analysis date: Mon Oct 30 22:40:38 GMT 2023
BAM file: SRX7354270.markdup.sorted.bam
Counting algorithm: uniquely-mapped-reads
GTF file: gencode.v44.annotation_genes_collapsed_only_patched_ERCC92.gtf
Number of bases for 5'-3' bias computation: 100
Number of transcripts for 5'-3' bias computation: 1,000
Paired-end sequencing: yes
Protocol: strand-specific-reverse
Sorting performed: yes

Summary 

Reads alignment

Number of mapped reads (left/right): 43,202,493 / 43,174,046
Number of aligned pairs (without duplicates): 43,168,864
Total number of alignments: 92,494,107
Number of secondary alignments: 6,117,568
Number of non-unique alignments: 10,020,271
Aligned to genes: 63,940,017
Ambiguous alignments: 235,535
No feature assigned: 17,759,121
Missing chromosome in annotation: 539,163
Not aligned: 4,295,981

Reads genomic origin

Exonic: 63,940,017 / 78.26%
Intronic: 10,038,079 / 12.29%
Intergenic: 7,721,042 / 9.45%
Intronic/intergenic overlapping exon: 2,938,616 / 3.6%

Transcript coverage profile

5' bias: 0.44
3' bias: 0.21
5'-3' bias: 2.14

Junction analysis

Reads at junctions: 25,502,424
ACCT 5.06%
AGGT 4.81%
AGGA 3.54%
ATCT 3.53%
TCCT 3.5%
GCCT 3.23%
AGCT 2.7%
CCCT 2.62%
AGGC 2.44%
TTCT 2.29%
AGAT 2.19%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis