Input data and parameters 

Input

Analysis date: Mon Oct 30 22:55:03 GMT 2023
BAM file: SRX7354226.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): 37,885,526 / 37,868,493
Number of aligned pairs (without duplicates): 37,863,836
Total number of alignments: 80,774,520
Number of secondary alignments: 5,020,501
Number of non-unique alignments: 8,222,554
Aligned to genes: 65,483,693
Ambiguous alignments: 172,093
No feature assigned: 6,522,625
Missing chromosome in annotation: 373,555
Not aligned: 2,432,783

Reads genomic origin

Exonic: 65,483,693 / 90.94%
Intronic: 4,039,644 / 5.61%
Intergenic: 2,482,981 / 3.45%
Intronic/intergenic overlapping exon: 2,229,404 / 3.1%

Transcript coverage profile

5' bias: 0.53
3' bias: 0.21
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 21,681,461
ACCT 5.09%
AGGT 4.94%
ATCT 3.95%
AGGA 3.78%
TCCT 3.78%
AGCT 3.02%
GCCT 2.7%
AGGC 2.36%
AGAT 2.21%
CCCT 2.18%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis