Input data and parameters 

Input

Analysis date: Tue Oct 31 17:30:30 GMT 2023
BAM file: SRX7354410.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): 32,362,823 / 32,343,261
Number of aligned pairs (without duplicates): 32,340,369
Total number of alignments: 68,535,463
Number of secondary alignments: 3,829,379
Number of non-unique alignments: 6,275,514
Aligned to genes: 54,063,854
Ambiguous alignments: 186,998
No feature assigned: 7,689,163
Missing chromosome in annotation: 319,934
Not aligned: 2,331,184

Reads genomic origin

Exonic: 54,063,854 / 87.55%
Intronic: 5,419,613 / 8.78%
Intergenic: 2,269,550 / 3.68%
Intronic/intergenic overlapping exon: 2,085,065 / 3.38%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.21
5'-3' bias: 1.9

Junction analysis

Reads at junctions: 17,123,116
ACCT 5.45%
AGGT 4.62%
ATCT 3.54%
TCCT 3.47%
AGGA 3.45%
GCCT 3.33%
AGCT 2.72%
CCCT 2.45%
AGGC 2.38%
AGAT 2.22%
TTCT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis