Input data and parameters 

Input

Analysis date: Tue Oct 31 09:53:24 GMT 2023
BAM file: SRX7354402.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): 34,159,486 / 34,105,407
Number of aligned pairs (without duplicates): 34,101,640
Total number of alignments: 73,367,407
Number of secondary alignments: 5,102,514
Number of non-unique alignments: 8,573,792
Aligned to genes: 57,701,489
Ambiguous alignments: 198,929
No feature assigned: 6,559,532
Missing chromosome in annotation: 333,665
Not aligned: 4,379,369

Reads genomic origin

Exonic: 57,701,489 / 89.79%
Intronic: 3,921,545 / 6.1%
Intergenic: 2,637,987 / 4.11%
Intronic/intergenic overlapping exon: 2,060,095 / 3.21%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.22
5'-3' bias: 1.9

Junction analysis

Reads at junctions: 17,746,189
ACCT 5.31%
AGGT 4.61%
ATCT 3.8%
TCCT 3.48%
AGGA 3.38%
GCCT 3.24%
AGCT 2.61%
CCCT 2.44%
TTCT 2.42%
AGGC 2.37%
AGAT 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