Input data and parameters 

Input

Analysis date: Tue Oct 31 15:57:03 GMT 2023
BAM file: SRX7354396.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): 31,621,771 / 31,440,637
Number of aligned pairs (without duplicates): 31,403,515
Total number of alignments: 69,129,373
Number of secondary alignments: 6,066,965
Number of non-unique alignments: 9,293,554
Aligned to genes: 44,775,556
Ambiguous alignments: 195,737
No feature assigned: 14,125,368
Missing chromosome in annotation: 739,158
Not aligned: 5,827,578

Reads genomic origin

Exonic: 44,775,556 / 76.02%
Intronic: 6,671,767 / 11.33%
Intergenic: 7,453,601 / 12.65%
Intronic/intergenic overlapping exon: 2,616,658 / 4.44%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.22
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 17,132,230
ACCT 5.17%
ATCT 4.6%
TCCT 4.51%
AGGT 4.25%
GCCT 3.45%
CCCT 2.87%
AGGA 2.87%
TTCT 2.47%
AGCT 2.24%
AGGC 2.05%
GTCT 2.04%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis