Input data and parameters 

Input

Analysis date: Mon Oct 30 12:41:04 GMT 2023
BAM file: SRX7354203.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): 33,431,998 / 33,410,133
Number of aligned pairs (without duplicates): 33,406,642
Total number of alignments: 70,308,917
Number of secondary alignments: 3,466,786
Number of non-unique alignments: 5,959,437
Aligned to genes: 56,532,785
Ambiguous alignments: 171,928
No feature assigned: 7,476,069
Missing chromosome in annotation: 168,698
Not aligned: 6,873,351

Reads genomic origin

Exonic: 56,532,785 / 88.32%
Intronic: 4,207,285 / 6.57%
Intergenic: 3,268,784 / 5.11%
Intronic/intergenic overlapping exon: 2,249,552 / 3.51%

Transcript coverage profile

5' bias: 0.24
3' bias: 0.12
5'-3' bias: 2.15

Junction analysis

Reads at junctions: 15,522,404
ACCT 5.52%
AGGT 4.91%
AGGA 3.75%
ATCT 3.7%
TCCT 3.46%
GCCT 3.09%
AGCT 2.72%
AGGC 2.37%
AGAT 2.37%
CCCT 2.31%
TTCT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis