Input data and parameters 

Input

Analysis date: Sun Oct 29 12:42:15 GMT 2023
BAM file: SRX7354147.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): 38,166,533 / 38,136,365
Number of aligned pairs (without duplicates): 38,131,931
Total number of alignments: 81,076,961
Number of secondary alignments: 4,774,063
Number of non-unique alignments: 7,892,544
Aligned to genes: 60,627,608
Ambiguous alignments: 260,879
No feature assigned: 11,921,810
Missing chromosome in annotation: 374,120
Not aligned: 5,729,070

Reads genomic origin

Exonic: 60,627,608 / 83.57%
Intronic: 7,234,347 / 9.97%
Intergenic: 4,687,463 / 6.46%
Intronic/intergenic overlapping exon: 2,826,480 / 3.9%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.31
5'-3' bias: 1.73

Junction analysis

Reads at junctions: 21,016,047
ACCT 5.14%
AGGT 4.7%
TCCT 3.71%
ATCT 3.5%
AGGA 3.46%
GCCT 3.39%
CCCT 2.73%
AGCT 2.69%
AGGC 2.48%
AGAT 2.14%
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