Input data and parameters 

Input

Analysis date: Sun Oct 29 01:23:41 GMT 2023
BAM file: SRX7354056.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): 34,899,189 / 34,876,402
Number of aligned pairs (without duplicates): 34,873,718
Total number of alignments: 74,435,635
Number of secondary alignments: 4,660,044
Number of non-unique alignments: 7,611,070
Aligned to genes: 58,528,694
Ambiguous alignments: 212,822
No feature assigned: 7,717,364
Missing chromosome in annotation: 365,685
Not aligned: 2,114,851

Reads genomic origin

Exonic: 58,528,694 / 88.35%
Intronic: 5,518,300 / 8.33%
Intergenic: 2,199,064 / 3.32%
Intronic/intergenic overlapping exon: 2,266,523 / 3.42%

Transcript coverage profile

5' bias: 0.37
3' bias: 0.22
5'-3' bias: 1.81

Junction analysis

Reads at junctions: 20,776,077
ACCT 5.35%
AGGT 4.53%
ATCT 3.77%
TCCT 3.6%
AGGA 3.35%
GCCT 3.34%
AGCT 2.68%
CCCT 2.42%
AGGC 2.36%
TTCT 2.15%
AGAT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis