Input data and parameters 

Input

Analysis date: Tue Oct 31 08:37:01 GMT 2023
BAM file: SRX7354310.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): 39,417,796 / 39,376,986
Number of aligned pairs (without duplicates): 39,369,619
Total number of alignments: 83,246,694
Number of secondary alignments: 4,451,912
Number of non-unique alignments: 7,527,701
Aligned to genes: 66,931,792
Ambiguous alignments: 247,433
No feature assigned: 8,324,170
Missing chromosome in annotation: 215,598
Not aligned: 10,898,286

Reads genomic origin

Exonic: 66,931,792 / 88.94%
Intronic: 5,454,985 / 7.25%
Intergenic: 2,869,185 / 3.81%
Intronic/intergenic overlapping exon: 2,771,791 / 3.68%

Transcript coverage profile

5' bias: 0.25
3' bias: 0.17
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 22,152,414
ACCT 5.73%
AGGT 4.67%
ATCT 3.79%
TCCT 3.61%
AGGA 3.3%
GCCT 3.28%
AGCT 2.55%
AGGC 2.44%
CCCT 2.32%
TTCT 2.05%
AGAT 2.03%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis