Input data and parameters 

Input

Analysis date: Mon Oct 30 11:05:56 GMT 2023
BAM file: SRX7354191.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): 38,516,620 / 38,499,364
Number of aligned pairs (without duplicates): 38,496,987
Total number of alignments: 81,446,660
Number of secondary alignments: 4,430,676
Number of non-unique alignments: 7,326,146
Aligned to genes: 65,949,352
Ambiguous alignments: 207,323
No feature assigned: 7,615,149
Missing chromosome in annotation: 348,690
Not aligned: 1,287,678

Reads genomic origin

Exonic: 65,949,352 / 89.65%
Intronic: 5,000,221 / 6.8%
Intergenic: 2,614,928 / 3.55%
Intronic/intergenic overlapping exon: 2,294,153 / 3.12%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.13
5'-3' bias: 2.05

Junction analysis

Reads at junctions: 22,196,643
ACCT 5.47%
AGGT 4.63%
GCCT 3.61%
AGGA 3.57%
ATCT 3.44%
TCCT 3.13%
AGCT 2.71%
AGGC 2.35%
TTCT 2.26%
AGAT 2.24%
CCCT 2.21%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis