Input data and parameters 

Input

Analysis date: Sun Oct 29 02:00:17 GMT 2023
BAM file: SRX7354072.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): 49,181,768 / 49,123,740
Number of aligned pairs (without duplicates): 49,114,821
Total number of alignments: 104,702,215
Number of secondary alignments: 6,396,707
Number of non-unique alignments: 10,367,089
Aligned to genes: 81,391,955
Ambiguous alignments: 295,939
No feature assigned: 12,099,327
Missing chromosome in annotation: 547,905
Not aligned: 11,638,060

Reads genomic origin

Exonic: 81,391,955 / 87.06%
Intronic: 7,611,904 / 8.14%
Intergenic: 4,487,423 / 4.8%
Intronic/intergenic overlapping exon: 3,387,779 / 3.62%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.21
5'-3' bias: 1.81

Junction analysis

Reads at junctions: 25,358,957
ACCT 5.51%
AGGT 4.63%
ATCT 3.76%
TCCT 3.66%
GCCT 3.36%
AGGA 3.25%
AGCT 2.6%
CCCT 2.55%
AGGC 2.4%
TTCT 2.23%
AGAT 2.06%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis