Input data and parameters 

Input

Analysis date: Mon Oct 30 22:32:26 GMT 2023
BAM file: SRX7354264.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): 30,295,332 / 30,277,361
Number of aligned pairs (without duplicates): 30,273,897
Total number of alignments: 64,293,821
Number of secondary alignments: 3,721,128
Number of non-unique alignments: 5,676,950
Aligned to genes: 48,761,861
Ambiguous alignments: 178,229
No feature assigned: 9,174,220
Missing chromosome in annotation: 502,561
Not aligned: 1,267,935

Reads genomic origin

Exonic: 48,761,861 / 84.16%
Intronic: 6,293,625 / 10.86%
Intergenic: 2,880,595 / 4.97%
Intronic/intergenic overlapping exon: 2,238,650 / 3.86%

Transcript coverage profile

5' bias: 0.52
3' bias: 0.25
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 18,223,811
ACCT 5.21%
AGGT 4.73%
TCCT 3.58%
ATCT 3.57%
AGGA 3.39%
GCCT 3.33%
AGCT 2.68%
CCCT 2.68%
AGGC 2.5%
TTCT 2.25%
AGAT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis