Input data and parameters 

Input

Analysis date: Mon Oct 30 09:39:56 GMT 2023
BAM file: SRX7354152.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): 43,784,563 / 43,746,651
Number of aligned pairs (without duplicates): 43,740,530
Total number of alignments: 92,675,529
Number of secondary alignments: 5,144,315
Number of non-unique alignments: 8,626,931
Aligned to genes: 71,690,800
Ambiguous alignments: 251,499
No feature assigned: 11,763,025
Missing chromosome in annotation: 343,274
Not aligned: 8,634,736

Reads genomic origin

Exonic: 71,690,800 / 85.9%
Intronic: 7,497,951 / 8.98%
Intergenic: 4,265,074 / 5.11%
Intronic/intergenic overlapping exon: 3,187,644 / 3.82%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.18
5'-3' bias: 1.79

Junction analysis

Reads at junctions: 22,059,751
ACCT 5.45%
AGGT 4.74%
AGGA 3.57%
ATCT 3.5%
TCCT 3.32%
GCCT 3.13%
AGCT 2.73%
AGGC 2.43%
CCCT 2.36%
AGAT 2.36%
TTCT 2.27%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis