Input data and parameters 

Input

Analysis date: Sun Oct 29 01:30:27 GMT 2023
BAM file: SRX7354054.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): 27,832,575 / 27,813,922
Number of aligned pairs (without duplicates): 27,810,680
Total number of alignments: 58,945,548
Number of secondary alignments: 3,299,051
Number of non-unique alignments: 5,345,654
Aligned to genes: 47,396,075
Ambiguous alignments: 166,979
No feature assigned: 5,729,011
Missing chromosome in annotation: 307,829
Not aligned: 1,993,029

Reads genomic origin

Exonic: 47,396,075 / 89.22%
Intronic: 3,666,499 / 6.9%
Intergenic: 2,062,512 / 3.88%
Intronic/intergenic overlapping exon: 1,909,329 / 3.59%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.18
5'-3' bias: 2.2

Junction analysis

Reads at junctions: 14,714,661
ACCT 5.54%
AGGT 4.61%
ATCT 3.81%
TCCT 3.55%
GCCT 3.51%
AGGA 3.34%
CCCT 2.5%
AGCT 2.49%
TTCT 2.36%
AGGC 2.34%
AGAT 2.01%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis