Input data and parameters 

Input

Analysis date: Sun Oct 29 02:16:44 GMT 2023
BAM file: SRX7354178.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): 46,933,012 / 46,877,524
Number of aligned pairs (without duplicates): 46,861,052
Total number of alignments: 103,700,501
Number of secondary alignments: 9,889,965
Number of non-unique alignments: 12,245,016
Aligned to genes: 75,869,105
Ambiguous alignments: 287,596
No feature assigned: 12,590,690
Missing chromosome in annotation: 2,708,094
Not aligned: 2,147,306

Reads genomic origin

Exonic: 75,869,105 / 85.77%
Intronic: 9,696,728 / 10.96%
Intergenic: 2,893,962 / 3.27%
Intronic/intergenic overlapping exon: 3,763,576 / 4.25%

Transcript coverage profile

5' bias: 0.49
3' bias: 0.2
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 28,165,505
ACCT 5.27%
AGGT 4.7%
ATCT 3.65%
TCCT 3.44%
AGGA 3.4%
GCCT 3.32%
AGCT 2.77%
CCCT 2.63%
AGGC 2.42%
AGAT 2.13%
TTCT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis