Input data and parameters 

Input

Analysis date: Sun Oct 29 01:42:54 GMT 2023
BAM file: SRX7354112.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): 37,369,237 / 37,337,032
Number of aligned pairs (without duplicates): 37,331,193
Total number of alignments: 79,003,454
Number of secondary alignments: 4,297,185
Number of non-unique alignments: 7,179,887
Aligned to genes: 61,284,155
Ambiguous alignments: 195,309
No feature assigned: 10,062,646
Missing chromosome in annotation: 281,457
Not aligned: 7,406,477

Reads genomic origin

Exonic: 61,284,155 / 85.9%
Intronic: 6,906,568 / 9.68%
Intergenic: 3,156,078 / 4.42%
Intronic/intergenic overlapping exon: 2,669,920 / 3.74%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.18
5'-3' bias: 1.86

Junction analysis

Reads at junctions: 19,800,143
ACCT 5.4%
AGGT 4.68%
ATCT 3.62%
AGGA 3.58%
TCCT 3.41%
GCCT 3.23%
AGCT 2.75%
AGGC 2.41%
CCCT 2.34%
AGAT 2.31%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis