Input data and parameters 

Input

Analysis date: Sun Oct 29 01:53:13 GMT 2023
BAM file: SRX7354136.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): 42,863,891 / 42,823,200
Number of aligned pairs (without duplicates): 42,817,518
Total number of alignments: 90,759,587
Number of secondary alignments: 5,072,496
Number of non-unique alignments: 8,584,494
Aligned to genes: 73,206,486
Ambiguous alignments: 257,821
No feature assigned: 8,427,612
Missing chromosome in annotation: 283,174
Not aligned: 8,308,007

Reads genomic origin

Exonic: 73,206,486 / 89.68%
Intronic: 4,991,353 / 6.11%
Intergenic: 3,436,259 / 4.21%
Intronic/intergenic overlapping exon: 2,800,341 / 3.43%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.17
5'-3' bias: 1.93

Junction analysis

Reads at junctions: 24,213,419
ACCT 5.43%
AGGT 4.63%
ATCT 3.65%
TCCT 3.48%
AGGA 3.42%
GCCT 3.36%
AGCT 2.67%
AGGC 2.47%
CCCT 2.34%
AGAT 2.15%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis