Input data and parameters 

Input

Analysis date: Sun Oct 29 01:34:04 GMT 2023
BAM file: SRX7354130.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): 31,335,323 / 31,316,968
Number of aligned pairs (without duplicates): 31,314,576
Total number of alignments: 67,496,646
Number of secondary alignments: 4,844,355
Number of non-unique alignments: 7,645,990
Aligned to genes: 50,352,379
Ambiguous alignments: 166,880
No feature assigned: 8,825,825
Missing chromosome in annotation: 505,572
Not aligned: 1,353,825

Reads genomic origin

Exonic: 50,352,379 / 85.09%
Intronic: 6,488,200 / 10.96%
Intergenic: 2,337,625 / 3.95%
Intronic/intergenic overlapping exon: 1,978,654 / 3.34%

Transcript coverage profile

5' bias: 0.46
3' bias: 0.22
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 15,526,091
ACCT 5.14%
AGGT 4.59%
ATCT 3.68%
AGGA 3.49%
TCCT 3.41%
GCCT 2.96%
AGCT 2.88%
CCCT 2.47%
AGGC 2.34%
TTCT 2.23%
AGAT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis