Input data and parameters 

Input

Analysis date: Mon Oct 30 22:37:10 GMT 2023
BAM file: SRX7354251.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): 38,353,926 / 38,335,712
Number of aligned pairs (without duplicates): 38,332,917
Total number of alignments: 80,800,224
Number of secondary alignments: 4,110,586
Number of non-unique alignments: 6,935,810
Aligned to genes: 64,523,474
Ambiguous alignments: 203,920
No feature assigned: 8,884,055
Missing chromosome in annotation: 252,965
Not aligned: 2,799,086

Reads genomic origin

Exonic: 64,523,474 / 87.9%
Intronic: 5,850,814 / 7.97%
Intergenic: 3,033,241 / 4.13%
Intronic/intergenic overlapping exon: 2,657,188 / 3.62%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.17
5'-3' bias: 2.15

Junction analysis

Reads at junctions: 20,519,120
ACCT 5.41%
AGGT 4.81%
ATCT 3.71%
AGGA 3.59%
TCCT 3.4%
GCCT 3.03%
AGCT 2.73%
CCCT 2.46%
AGGC 2.41%
AGAT 2.3%
TTCT 2.07%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis