Input data and parameters 

Input

Analysis date: Sun Oct 29 01:11:57 GMT 2023
BAM file: SRX7354101.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): 30,575,032 / 30,474,505
Number of aligned pairs (without duplicates): 30,460,099
Total number of alignments: 64,880,934
Number of secondary alignments: 3,831,397
Number of non-unique alignments: 6,518,319
Aligned to genes: 50,875,929
Ambiguous alignments: 185,694
No feature assigned: 7,129,641
Missing chromosome in annotation: 171,351
Not aligned: 11,590,159

Reads genomic origin

Exonic: 50,875,929 / 87.71%
Intronic: 4,139,631 / 7.14%
Intergenic: 2,990,010 / 5.15%
Intronic/intergenic overlapping exon: 2,042,604 / 3.52%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.18
5'-3' bias: 2.36

Junction analysis

Reads at junctions: 16,141,318
ACCT 5.7%
AGGT 4.73%
ATCT 3.8%
TCCT 3.72%
AGGA 3.46%
GCCT 3.16%
CCCT 2.58%
AGCT 2.51%
AGGC 2.32%
AGAT 2.1%
TTCT 2.06%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis