Input data and parameters 

Input

Analysis date: Tue Oct 31 09:30:18 GMT 2023
BAM file: SRX7354222.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): 40,893,502 / 40,631,754
Number of aligned pairs (without duplicates): 40,611,840
Total number of alignments: 87,391,881
Number of secondary alignments: 5,866,625
Number of non-unique alignments: 9,759,314
Aligned to genes: 58,940,846
Ambiguous alignments: 205,593
No feature assigned: 18,038,376
Missing chromosome in annotation: 447,752
Not aligned: 17,870,614

Reads genomic origin

Exonic: 58,940,846 / 76.57%
Intronic: 8,827,496 / 11.47%
Intergenic: 9,210,880 / 11.97%
Intronic/intergenic overlapping exon: 3,676,854 / 4.78%

Transcript coverage profile

5' bias: 0.47
3' bias: 0.22
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 21,940,049
ACCT 5.29%
AGGT 4.69%
TCCT 3.5%
ATCT 3.41%
GCCT 3.34%
AGGA 3.34%
AGCT 2.78%
CCCT 2.47%
AGGC 2.39%
TTCT 2.29%
AGAT 2.14%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis