Input data and parameters 

Input

Analysis date: Tue Oct 31 16:41:49 GMT 2023
BAM file: SRX7354393.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): 126,093,945 / 125,926,247
Number of aligned pairs (without duplicates): 125,914,605
Total number of alignments: 270,928,955
Number of secondary alignments: 18,908,763
Number of non-unique alignments: 30,390,501
Aligned to genes: 215,128,352
Ambiguous alignments: 967,544
No feature assigned: 22,773,118
Missing chromosome in annotation: 1,669,440
Not aligned: 11,107,986

Reads genomic origin

Exonic: 215,128,352 / 90.43%
Intronic: 15,319,157 / 6.44%
Intergenic: 7,453,961 / 3.13%
Intronic/intergenic overlapping exon: 8,993,078 / 3.78%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.22
5'-3' bias: 1.71

Junction analysis

Reads at junctions: 78,567,120
ACCT 5.38%
AGGT 4.39%
ATCT 4.1%
TCCT 3.98%
GCCT 3.51%
AGGA 3.12%
CCCT 2.75%
TTCT 2.51%
AGCT 2.48%
AGGC 2.29%
AGAT 1.9%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis