Input data and parameters 

Input

Analysis date: Sun Oct 29 01:40:44 GMT 2023
BAM file: SRX7354102.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): 30,076,716 / 30,054,357
Number of aligned pairs (without duplicates): 30,051,643
Total number of alignments: 65,234,475
Number of secondary alignments: 5,103,402
Number of non-unique alignments: 7,138,623
Aligned to genes: 49,286,293
Ambiguous alignments: 171,429
No feature assigned: 7,688,363
Missing chromosome in annotation: 949,767
Not aligned: 3,301,137

Reads genomic origin

Exonic: 49,286,293 / 86.51%
Intronic: 5,449,698 / 9.57%
Intergenic: 2,238,665 / 3.93%
Intronic/intergenic overlapping exon: 1,926,888 / 3.38%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.21
5'-3' bias: 2.04

Junction analysis

Reads at junctions: 15,160,237
ACCT 5.53%
AGGT 4.75%
ATCT 3.68%
AGGA 3.62%
TCCT 3.6%
GCCT 3.17%
AGCT 2.73%
CCCT 2.39%
AGGC 2.35%
AGAT 2.27%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis