Input data and parameters 

Input

Analysis date: Mon Oct 30 11:14:48 GMT 2023
BAM file: SRX7354170.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): 24,267,084 / 24,253,501
Number of aligned pairs (without duplicates): 24,249,879
Total number of alignments: 52,226,663
Number of secondary alignments: 3,706,078
Number of non-unique alignments: 6,342,544
Aligned to genes: 39,523,490
Ambiguous alignments: 98,501
No feature assigned: 6,036,550
Missing chromosome in annotation: 225,578
Not aligned: 1,365,875

Reads genomic origin

Exonic: 39,523,490 / 86.75%
Intronic: 3,354,052 / 7.36%
Intergenic: 2,682,498 / 5.89%
Intronic/intergenic overlapping exon: 1,777,156 / 3.9%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.13
5'-3' bias: 2.35

Junction analysis

Reads at junctions: 8,078,529
ACCT 5.25%
AGGT 4.62%
ATCT 3.64%
AGGA 3.51%
TCCT 3.4%
GCCT 3.26%
AGCT 2.64%
TTCT 2.39%
CCCT 2.31%
AGGC 2.24%
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