Input data and parameters 

Input

Analysis date: Mon Oct 30 09:32:57 GMT 2023
BAM file: SRX7354182.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): 35,894,703 / 35,836,714
Number of aligned pairs (without duplicates): 35,826,008
Total number of alignments: 76,153,681
Number of secondary alignments: 4,422,264
Number of non-unique alignments: 7,276,545
Aligned to genes: 58,668,088
Ambiguous alignments: 197,815
No feature assigned: 9,703,473
Missing chromosome in annotation: 307,760
Not aligned: 18,366,931

Reads genomic origin

Exonic: 58,668,088 / 85.81%
Intronic: 6,506,344 / 9.52%
Intergenic: 3,197,129 / 4.68%
Intronic/intergenic overlapping exon: 2,551,209 / 3.73%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.2
5'-3' bias: 2.13

Junction analysis

Reads at junctions: 20,735,196
ACCT 5.36%
AGGT 4.9%
AGGA 3.64%
ATCT 3.57%
TCCT 3.51%
GCCT 2.77%
AGCT 2.73%
AGGC 2.47%
CCCT 2.35%
AGAT 2.28%
TTCT 2.02%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis