Input data and parameters 

Input

Analysis date: Sun Oct 29 01:45:13 GMT 2023
BAM file: SRX7354100.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): 42,907,737 / 42,873,796
Number of aligned pairs (without duplicates): 42,864,362
Total number of alignments: 92,994,472
Number of secondary alignments: 7,212,939
Number of non-unique alignments: 11,525,659
Aligned to genes: 73,128,212
Ambiguous alignments: 262,473
No feature assigned: 7,325,431
Missing chromosome in annotation: 752,697
Not aligned: 3,021,345

Reads genomic origin

Exonic: 73,128,212 / 90.89%
Intronic: 4,641,559 / 5.77%
Intergenic: 2,683,872 / 3.34%
Intronic/intergenic overlapping exon: 2,656,827 / 3.3%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.23
5'-3' bias: 1.79

Junction analysis

Reads at junctions: 22,030,480
AGGT 5.03%
ACCT 5.02%
AGGA 3.6%
TCCT 3.6%
ATCT 3.52%
GCCT 2.68%
AGCT 2.62%
AGGC 2.47%
CCCT 2.44%
AGAT 2.1%
TTCT 2.02%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis