Input data and parameters 

Input

Analysis date: Mon Oct 30 12:50:30 GMT 2023
BAM file: SRX7354204.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): 47,007,698 / 46,965,345
Number of aligned pairs (without duplicates): 46,958,020
Total number of alignments: 99,501,785
Number of secondary alignments: 5,528,742
Number of non-unique alignments: 9,254,356
Aligned to genes: 77,630,490
Ambiguous alignments: 281,942
No feature assigned: 12,002,980
Missing chromosome in annotation: 332,017
Not aligned: 11,403,601

Reads genomic origin

Exonic: 77,630,490 / 86.61%
Intronic: 7,854,947 / 8.76%
Intergenic: 4,148,033 / 4.63%
Intronic/intergenic overlapping exon: 3,244,181 / 3.62%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.18
5'-3' bias: 2.01

Junction analysis

Reads at junctions: 25,195,707
ACCT 5.25%
AGGT 4.94%
AGGA 3.8%
TCCT 3.52%
ATCT 3.45%
GCCT 2.84%
AGCT 2.72%
CCCT 2.45%
AGGC 2.43%
AGAT 2.42%
TTCT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis