Input data and parameters 

Input

Analysis date: Tue Oct 31 09:03:03 GMT 2023
BAM file: SRX7354321.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): 42,420,841 / 42,397,165
Number of aligned pairs (without duplicates): 42,388,957
Total number of alignments: 91,580,762
Number of secondary alignments: 6,762,756
Number of non-unique alignments: 10,660,394
Aligned to genes: 72,587,512
Ambiguous alignments: 254,206
No feature assigned: 7,356,937
Missing chromosome in annotation: 721,713
Not aligned: 3,302,606

Reads genomic origin

Exonic: 72,587,512 / 90.8%
Intronic: 4,097,279 / 5.13%
Intergenic: 3,259,658 / 4.08%
Intronic/intergenic overlapping exon: 3,424,818 / 4.28%

Transcript coverage profile

5' bias: 0.06
3' bias: 0.08
5'-3' bias: 2.29

Junction analysis

Reads at junctions: 21,388,301
ACCT 5.86%
TCCT 4.92%
ATCT 4.68%
AGGT 4.22%
CCCT 3.67%
AGGA 2.94%
GCCT 2.44%
AGGC 2.29%
TCCC 2.28%
AGAC 2.17%
CCCA 2.02%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis