Input data and parameters 

Input

Analysis date: Tue Oct 31 17:17:45 GMT 2023
BAM file: SRX7354408.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): 35,615,661 / 35,584,685
Number of aligned pairs (without duplicates): 35,581,893
Total number of alignments: 75,220,298
Number of secondary alignments: 4,019,952
Number of non-unique alignments: 6,836,677
Aligned to genes: 59,595,720
Ambiguous alignments: 198,524
No feature assigned: 8,359,462
Missing chromosome in annotation: 229,915
Not aligned: 4,317,470

Reads genomic origin

Exonic: 59,595,720 / 87.7%
Intronic: 5,676,197 / 8.35%
Intergenic: 2,683,265 / 3.95%
Intronic/intergenic overlapping exon: 2,278,206 / 3.35%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.18
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 19,615,740
ACCT 5.52%
AGGT 4.69%
ATCT 3.56%
AGGA 3.51%
TCCT 3.4%
GCCT 3.28%
AGCT 2.72%
AGGC 2.41%
AGAT 2.35%
CCCT 2.33%
TTCT 2.26%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis