Input data and parameters 

Input

Analysis date: Tue Oct 31 08:56:48 GMT 2023
BAM file: SRX7354294.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): 34,593,274 / 34,576,478
Number of aligned pairs (without duplicates): 34,573,819
Total number of alignments: 73,369,404
Number of secondary alignments: 4,199,652
Number of non-unique alignments: 6,892,288
Aligned to genes: 57,625,501
Ambiguous alignments: 223,138
No feature assigned: 8,323,379
Missing chromosome in annotation: 305,098
Not aligned: 1,433,794

Reads genomic origin

Exonic: 57,625,501 / 87.38%
Intronic: 6,115,455 / 9.27%
Intergenic: 2,207,924 / 3.35%
Intronic/intergenic overlapping exon: 2,190,900 / 3.32%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.18
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 19,560,796
ACCT 5.49%
AGGT 4.65%
ATCT 3.57%
AGGA 3.56%
TCCT 3.35%
GCCT 3.34%
AGCT 2.74%
CCCT 2.41%
AGGC 2.4%
AGAT 2.28%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis