Input data and parameters 

Input

Analysis date: Tue Oct 31 09:59:00 GMT 2023
BAM file: SRX7354387.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): 30,788,458 / 30,763,449
Number of aligned pairs (without duplicates): 30,758,537
Total number of alignments: 66,871,404
Number of secondary alignments: 5,319,497
Number of non-unique alignments: 7,533,256
Aligned to genes: 50,622,681
Ambiguous alignments: 178,517
No feature assigned: 7,573,315
Missing chromosome in annotation: 963,635
Not aligned: 3,529,367

Reads genomic origin

Exonic: 50,622,681 / 86.99%
Intronic: 4,878,184 / 8.38%
Intergenic: 2,695,131 / 4.63%
Intronic/intergenic overlapping exon: 2,057,971 / 3.54%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.24
5'-3' bias: 1.8

Junction analysis

Reads at junctions: 16,259,498
ACCT 5.22%
AGGT 4.6%
ATCT 3.73%
TCCT 3.39%
AGGA 3.35%
TTCT 3.33%
GCCT 2.99%
AGCT 2.68%
CCCT 2.43%
AGGC 2.27%
AGAT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis