Input data and parameters 

Input

Analysis date: Tue Oct 31 09:46:18 GMT 2023
BAM file: SRX7354337.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): 45,382,998 / 45,357,785
Number of aligned pairs (without duplicates): 45,349,717
Total number of alignments: 98,239,566
Number of secondary alignments: 7,498,783
Number of non-unique alignments: 11,755,771
Aligned to genes: 77,851,350
Ambiguous alignments: 337,985
No feature assigned: 7,428,333
Missing chromosome in annotation: 866,127
Not aligned: 3,206,967

Reads genomic origin

Exonic: 77,851,350 / 91.29%
Intronic: 4,084,640 / 4.79%
Intergenic: 3,343,693 / 3.92%
Intronic/intergenic overlapping exon: 4,046,270 / 4.74%

Transcript coverage profile

5' bias: 0.09
3' bias: 0.11
5'-3' bias: 2.35

Junction analysis

Reads at junctions: 27,388,871
TCCT 6.45%
ACCT 5.67%
ATCT 4.76%
AGGT 3.82%
CCCT 3.77%
AGGA 2.62%
TCCC 2.47%
GCCT 2.34%
CGTA 2.22%
AGGC 2.22%
GTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis