Input data and parameters 

Input

Analysis date: Sun Oct 29 01:32:07 GMT 2023
BAM file: SRX7354159.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): 42,291,419 / 42,204,373
Number of aligned pairs (without duplicates): 42,193,568
Total number of alignments: 91,808,775
Number of secondary alignments: 7,312,983
Number of non-unique alignments: 10,951,641
Aligned to genes: 71,391,544
Ambiguous alignments: 314,096
No feature assigned: 8,080,574
Missing chromosome in annotation: 1,070,920
Not aligned: 10,989,214

Reads genomic origin

Exonic: 71,391,544 / 89.83%
Intronic: 4,658,783 / 5.86%
Intergenic: 3,421,791 / 4.31%
Intronic/intergenic overlapping exon: 3,937,813 / 4.95%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.1
5'-3' bias: 2.32

Junction analysis

Reads at junctions: 22,436,340
TCCT 6.03%
ACCT 5.48%
ATCT 4.83%
CCCT 3.92%
AGGT 3.88%
AGGA 2.72%
GCCT 2.31%
TCCC 2.27%
AGGC 2.22%
GTCT 2.14%
TTCT 1.94%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis