Input data and parameters 

Input

Analysis date: Mon Oct 30 22:57:09 GMT 2023
BAM file: SRX7354283.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): 42,649,122 / 42,613,151
Number of aligned pairs (without duplicates): 42,608,922
Total number of alignments: 90,274,213
Number of secondary alignments: 5,011,940
Number of non-unique alignments: 8,354,323
Aligned to genes: 72,315,358
Ambiguous alignments: 243,279
No feature assigned: 8,991,031
Missing chromosome in annotation: 370,222
Not aligned: 2,996,667

Reads genomic origin

Exonic: 72,315,358 / 88.94%
Intronic: 5,750,993 / 7.07%
Intergenic: 3,240,038 / 3.98%
Intronic/intergenic overlapping exon: 2,943,711 / 3.62%

Transcript coverage profile

5' bias: 0.45
3' bias: 0.15
5'-3' bias: 2.11

Junction analysis

Reads at junctions: 25,562,411
ACCT 5.42%
AGGT 4.85%
AGGA 3.75%
ATCT 3.56%
TCCT 3.43%
GCCT 2.88%
AGCT 2.71%
AGGC 2.42%
CCCT 2.34%
AGAT 2.33%
TTCT 2.25%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis