Input data and parameters 

Input

Analysis date: Tue Oct 31 01:46:02 GMT 2023
BAM file: SRX7354273.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): 56,403,401 / 56,389,292
Number of aligned pairs (without duplicates): 56,386,297
Total number of alignments: 122,383,193
Number of secondary alignments: 9,590,500
Number of non-unique alignments: 15,218,940
Aligned to genes: 80,785,428
Ambiguous alignments: 279,689
No feature assigned: 25,048,532
Missing chromosome in annotation: 1,050,604
Not aligned: 1,266,567

Reads genomic origin

Exonic: 80,785,428 / 76.33%
Intronic: 11,892,032 / 11.24%
Intergenic: 13,156,500 / 12.43%
Intronic/intergenic overlapping exon: 3,434,460 / 3.25%

Transcript coverage profile

5' bias: 0.5
3' bias: 0.22
5'-3' bias: 1.88

Junction analysis

Reads at junctions: 31,615,124
ACCT 4.79%
AGGT 4.49%
ATCT 3.67%
TCCT 3.58%
AGGA 3.39%
GCCT 3.33%
CCCT 2.71%
AGCT 2.6%
TTCT 2.44%
AGGC 2.27%
AGAT 2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis