Input data and parameters 

Input

Analysis date: Mon Oct 30 09:43:55 GMT 2023
BAM file: SRX7354087.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): 65,372,906 / 65,284,004
Number of aligned pairs (without duplicates): 65,276,619
Total number of alignments: 138,820,358
Number of secondary alignments: 8,163,448
Number of non-unique alignments: 13,084,272
Aligned to genes: 101,575,831
Ambiguous alignments: 363,951
No feature assigned: 22,957,720
Missing chromosome in annotation: 838,584
Not aligned: 10,776,242

Reads genomic origin

Exonic: 101,575,831 / 81.57%
Intronic: 13,699,127 / 11%
Intergenic: 9,258,593 / 7.43%
Intronic/intergenic overlapping exon: 5,146,393 / 4.13%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.3
5'-3' bias: 1.69

Junction analysis

Reads at junctions: 33,498,862
ACCT 4.99%
AGGT 4.79%
TCCT 3.69%
ATCT 3.57%
AGGA 3.45%
GCCT 3.17%
CCCT 2.79%
AGCT 2.76%
AGGC 2.53%
TTCT 2.01%
AGAT 2.01%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis