Input data and parameters 

Input

Analysis date: Mon Oct 30 20:26:31 GMT 2023
BAM file: SRX7354239.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): 34,649,226 / 34,625,806
Number of aligned pairs (without duplicates): 34,622,944
Total number of alignments: 73,954,372
Number of secondary alignments: 4,679,340
Number of non-unique alignments: 7,872,920
Aligned to genes: 58,862,729
Ambiguous alignments: 217,610
No feature assigned: 6,725,420
Missing chromosome in annotation: 275,693
Not aligned: 2,842,106

Reads genomic origin

Exonic: 58,862,729 / 89.75%
Intronic: 4,435,457 / 6.76%
Intergenic: 2,289,963 / 3.49%
Intronic/intergenic overlapping exon: 1,952,698 / 2.98%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.18
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 19,287,984
ACCT 5.68%
AGGT 4.99%
AGGA 3.72%
TCCT 3.48%
ATCT 3.47%
GCCT 3.06%
AGCT 2.74%
CCCT 2.44%
AGGC 2.41%
AGAT 2.27%
TTCT 2.14%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis