Input data and parameters 

Input

Analysis date: Sun Oct 29 01:53:20 GMT 2023
BAM file: SRX7354115.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): 29,838,298 / 29,818,055
Number of aligned pairs (without duplicates): 29,814,529
Total number of alignments: 63,476,624
Number of secondary alignments: 3,820,271
Number of non-unique alignments: 6,156,535
Aligned to genes: 47,510,332
Ambiguous alignments: 198,770
No feature assigned: 9,281,809
Missing chromosome in annotation: 329,178
Not aligned: 3,143,329

Reads genomic origin

Exonic: 47,510,332 / 83.66%
Intronic: 6,498,077 / 11.44%
Intergenic: 2,783,732 / 4.9%
Intronic/intergenic overlapping exon: 2,202,608 / 3.88%

Transcript coverage profile

5' bias: 0.54
3' bias: 0.29
5'-3' bias: 1.78

Junction analysis

Reads at junctions: 18,577,065
ACCT 5.09%
AGGT 4.78%
AGGA 3.48%
TCCT 3.43%
ATCT 3.33%
GCCT 3.13%
AGCT 2.83%
CCCT 2.55%
AGGC 2.42%
TTCT 2.21%
AGAT 2.19%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis