Input data and parameters 

Input

Analysis date: Tue Oct 31 09:30:26 GMT 2023
BAM file: SRX7354278.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): 47,216,611 / 47,191,863
Number of aligned pairs (without duplicates): 47,179,225
Total number of alignments: 101,573,965
Number of secondary alignments: 7,165,491
Number of non-unique alignments: 11,121,565
Aligned to genes: 80,856,676
Ambiguous alignments: 344,616
No feature assigned: 8,435,569
Missing chromosome in annotation: 815,539
Not aligned: 3,847,554

Reads genomic origin

Exonic: 80,856,676 / 90.55%
Intronic: 5,166,134 / 5.79%
Intergenic: 3,269,435 / 3.66%
Intronic/intergenic overlapping exon: 3,864,103 / 4.33%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.13
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 27,218,368
TCCT 5.73%
ACCT 5.54%
ATCT 4.84%
AGGT 4.02%
CCCT 3.21%
AGGA 2.79%
GCCT 2.44%
AGGC 2.31%
TCCC 2.2%
AGCT 1.97%
TTCT 1.92%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis