Input data and parameters 

Input

Analysis date: Sun Oct 29 01:41:32 GMT 2023
BAM file: SRX7354058.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): 30,722,676 / 30,707,289
Number of aligned pairs (without duplicates): 30,704,237
Total number of alignments: 65,730,560
Number of secondary alignments: 4,300,595
Number of non-unique alignments: 7,056,188
Aligned to genes: 50,268,696
Ambiguous alignments: 184,759
No feature assigned: 7,883,428
Missing chromosome in annotation: 337,489
Not aligned: 2,711,309

Reads genomic origin

Exonic: 50,268,696 / 86.44%
Intronic: 5,910,722 / 10.16%
Intergenic: 1,972,706 / 3.39%
Intronic/intergenic overlapping exon: 1,884,440 / 3.24%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.2
5'-3' bias: 2

Junction analysis

Reads at junctions: 16,152,495
ACCT 5.26%
AGGT 4.69%
ATCT 3.56%
AGGA 3.5%
TCCT 3.49%
GCCT 3.03%
AGCT 2.7%
TTCT 2.52%
CCCT 2.35%
AGGC 2.34%
AGAT 2.31%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis