Input data and parameters 

Input

Analysis date: Sun Oct 29 01:40:57 GMT 2023
BAM file: SRX7354133.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): 42,445,626 / 42,407,722
Number of aligned pairs (without duplicates): 42,378,182
Total number of alignments: 90,662,577
Number of secondary alignments: 5,809,229
Number of non-unique alignments: 9,632,655
Aligned to genes: 72,557,657
Ambiguous alignments: 305,713
No feature assigned: 7,676,029
Missing chromosome in annotation: 490,523
Not aligned: 3,006,678

Reads genomic origin

Exonic: 72,557,657 / 90.43%
Intronic: 4,109,963 / 5.12%
Intergenic: 3,566,066 / 4.44%
Intronic/intergenic overlapping exon: 3,199,382 / 3.99%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.22
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 22,718,935
ACCT 4.95%
AGGT 4.71%
ATCT 4.3%
TCCT 3.95%
GCCT 3.43%
AGGA 3.2%
CCCT 2.77%
AGCT 2.49%
TTCT 2.4%
AGGC 2.3%
AGAA 1.85%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis