Input data and parameters 

Input

Analysis date: Sun Oct 29 12:14:38 GMT 2023
BAM file: SRX7354131.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): 57,394,953 / 57,353,995
Number of aligned pairs (without duplicates): 57,348,042
Total number of alignments: 122,185,770
Number of secondary alignments: 7,436,822
Number of non-unique alignments: 12,412,179
Aligned to genes: 92,062,463
Ambiguous alignments: 314,697
No feature assigned: 16,915,742
Missing chromosome in annotation: 480,689
Not aligned: 4,107,292

Reads genomic origin

Exonic: 92,062,463 / 84.48%
Intronic: 11,877,722 / 10.9%
Intergenic: 5,038,020 / 4.62%
Intronic/intergenic overlapping exon: 3,915,960 / 3.59%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.18
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 28,412,628
ACCT 5.34%
AGGT 4.66%
ATCT 3.67%
AGGA 3.66%
TCCT 3.51%
GCCT 3.18%
AGCT 2.65%
CCCT 2.45%
AGAT 2.39%
AGGC 2.37%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis