Input data and parameters 

Input

Analysis date: Tue Oct 31 09:47:38 GMT 2023
BAM file: SRX7354375.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): 33,010,145 / 32,958,052
Number of aligned pairs (without duplicates): 32,952,477
Total number of alignments: 70,343,994
Number of secondary alignments: 4,375,797
Number of non-unique alignments: 7,131,501
Aligned to genes: 53,019,891
Ambiguous alignments: 199,840
No feature assigned: 9,655,653
Missing chromosome in annotation: 337,109
Not aligned: 4,806,065

Reads genomic origin

Exonic: 53,019,891 / 84.59%
Intronic: 5,685,968 / 9.07%
Intergenic: 3,969,685 / 6.33%
Intronic/intergenic overlapping exon: 2,229,052 / 3.56%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.3
5'-3' bias: 1.65

Junction analysis

Reads at junctions: 20,300,477
ACCT 5.21%
AGGT 4.8%
TCCT 3.64%
AGGA 3.45%
ATCT 3.44%
GCCT 3.06%
AGCT 2.68%
CCCT 2.47%
AGGC 2.41%
AGAT 2.14%
TTCT 2.06%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis