Input data and parameters 

Input

Analysis date: Mon Oct 30 12:47:21 GMT 2023
BAM file: SRX7354201.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): 29,560,511 / 29,543,548
Number of aligned pairs (without duplicates): 29,540,619
Total number of alignments: 62,870,923
Number of secondary alignments: 3,766,864
Number of non-unique alignments: 6,136,730
Aligned to genes: 49,910,603
Ambiguous alignments: 180,739
No feature assigned: 6,304,607
Missing chromosome in annotation: 338,244
Not aligned: 3,592,527

Reads genomic origin

Exonic: 49,910,603 / 88.78%
Intronic: 4,244,244 / 7.55%
Intergenic: 2,060,363 / 3.67%
Intronic/intergenic overlapping exon: 1,752,121 / 3.12%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.21
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 15,431,333
ACCT 5.38%
AGGT 4.72%
AGGA 3.55%
ATCT 3.53%
TCCT 3.51%
GCCT 3.22%
AGCT 2.71%
CCCT 2.48%
AGGC 2.38%
AGAT 2.21%
TTCT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis