Input data and parameters 

Input

Analysis date: Tue Oct 31 15:49:10 GMT 2023
BAM file: SRX7354414.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): 58,554,816 / 58,525,802
Number of aligned pairs (without duplicates): 58,515,123
Total number of alignments: 132,247,847
Number of secondary alignments: 15,167,229
Number of non-unique alignments: 18,913,450
Aligned to genes: 95,729,342
Ambiguous alignments: 565,887
No feature assigned: 13,024,829
Missing chromosome in annotation: 4,014,339
Not aligned: 3,035,444

Reads genomic origin

Exonic: 95,729,342 / 88.02%
Intronic: 9,685,508 / 8.91%
Intergenic: 3,339,321 / 3.07%
Intronic/intergenic overlapping exon: 5,609,166 / 5.16%

Transcript coverage profile

5' bias: 0.22
3' bias: 0.16
5'-3' bias: 1.92

Junction analysis

Reads at junctions: 37,442,004
ACCT 4.87%
TCCT 4.78%
ATCT 4.53%
AGGT 4.44%
CCCT 3.53%
AGGA 3.46%
GCCT 3.06%
AGCT 2.15%
AGGC 2.09%
TTCT 2.04%
AGAA 1.8%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis