Input data and parameters 

Input

Analysis date: Mon Oct 30 22:58:28 GMT 2023
BAM file: SRX7354281.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): 37,526,378 / 37,512,103
Number of aligned pairs (without duplicates): 37,506,184
Total number of alignments: 80,776,508
Number of secondary alignments: 5,738,027
Number of non-unique alignments: 9,339,493
Aligned to genes: 64,335,667
Ambiguous alignments: 242,768
No feature assigned: 6,352,539
Missing chromosome in annotation: 506,041
Not aligned: 3,729,815

Reads genomic origin

Exonic: 64,335,667 / 91.01%
Intronic: 3,546,037 / 5.02%
Intergenic: 2,806,502 / 3.97%
Intronic/intergenic overlapping exon: 2,478,877 / 3.51%

Transcript coverage profile

5' bias: 0.22
3' bias: 0.14
5'-3' bias: 2.29

Junction analysis

Reads at junctions: 19,390,930
ACCT 5.09%
AGGT 4.77%
ATCT 4.32%
TCCT 4.21%
AGGA 3.29%
CCCT 2.92%
GCCT 2.83%
AGCT 2.31%
AGGC 2.22%
TTCT 2.1%
AGAA 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis