Input data and parameters 

Input

Analysis date: Sun Oct 29 01:10:02 GMT 2023
BAM file: SRX7354052.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): 31,087,757 / 31,067,692
Number of aligned pairs (without duplicates): 31,064,530
Total number of alignments: 66,004,632
Number of secondary alignments: 3,849,183
Number of non-unique alignments: 6,351,084
Aligned to genes: 50,607,204
Ambiguous alignments: 187,167
No feature assigned: 8,598,057
Missing chromosome in annotation: 261,120
Not aligned: 2,653,343

Reads genomic origin

Exonic: 50,607,204 / 85.48%
Intronic: 6,522,209 / 11.02%
Intergenic: 2,075,848 / 3.51%
Intronic/intergenic overlapping exon: 2,037,765 / 3.44%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.18
5'-3' bias: 2.28

Junction analysis

Reads at junctions: 17,036,006
ACCT 5.42%
AGGT 4.69%
TCCT 3.61%
AGGA 3.59%
ATCT 3.49%
GCCT 2.97%
AGCT 2.69%
AGGC 2.38%
AGAT 2.31%
CCCT 2.3%
AGGG 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis