Input data and parameters 

Input

Analysis date: Tue Oct 31 01:36:52 GMT 2023
BAM file: SRX7354293.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): 29,193,752 / 29,176,535
Number of aligned pairs (without duplicates): 29,172,597
Total number of alignments: 61,630,413
Number of secondary alignments: 3,260,126
Number of non-unique alignments: 5,400,306
Aligned to genes: 48,729,914
Ambiguous alignments: 147,920
No feature assigned: 7,122,336
Missing chromosome in annotation: 229,937
Not aligned: 3,859,059

Reads genomic origin

Exonic: 48,729,914 / 87.25%
Intronic: 4,849,464 / 8.68%
Intergenic: 2,272,872 / 4.07%
Intronic/intergenic overlapping exon: 1,719,920 / 3.08%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.13
5'-3' bias: 2.36

Junction analysis

Reads at junctions: 14,955,335
ACCT 5.41%
AGGT 4.74%
ATCT 3.83%
AGGA 3.65%
TCCT 3.63%
GCCT 3.02%
AGCT 2.63%
AGGC 2.36%
CCCT 2.34%
AGAT 2.26%
TTCT 2.21%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis