Input data and parameters 

Input

Analysis date: Tue Oct 31 09:32:30 GMT 2023
BAM file: SRX7354306.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): 74,436,389 / 74,382,890
Number of aligned pairs (without duplicates): 74,373,190
Total number of alignments: 159,970,734
Number of secondary alignments: 11,151,455
Number of non-unique alignments: 16,050,091
Aligned to genes: 130,152,536
Ambiguous alignments: 592,704
No feature assigned: 11,231,764
Missing chromosome in annotation: 1,943,639
Not aligned: 4,123,807

Reads genomic origin

Exonic: 130,152,536 / 92.06%
Intronic: 6,605,421 / 4.67%
Intergenic: 4,626,343 / 3.27%
Intronic/intergenic overlapping exon: 5,498,545 / 3.89%

Transcript coverage profile

5' bias: 0.16
3' bias: 0.15
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 49,983,960
ACCT 5.27%
TCCT 4.68%
AGGT 4.32%
ATCT 4.18%
CCCT 3.2%
AGGA 2.85%
AGGC 2.45%
GCCT 2.42%
AGCT 2.14%
TTCT 1.9%
GTCT 1.84%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis