Input data and parameters 

Input

Analysis date: Mon Oct 30 13:01:20 GMT 2023
BAM file: SRX7354197.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): 43,685,919 / 43,663,152
Number of aligned pairs (without duplicates): 43,655,439
Total number of alignments: 94,007,562
Number of secondary alignments: 6,658,491
Number of non-unique alignments: 10,516,551
Aligned to genes: 74,543,795
Ambiguous alignments: 287,933
No feature assigned: 7,993,083
Missing chromosome in annotation: 666,200
Not aligned: 1,796,643

Reads genomic origin

Exonic: 74,543,795 / 90.32%
Intronic: 5,294,511 / 6.41%
Intergenic: 2,698,572 / 3.27%
Intronic/intergenic overlapping exon: 3,211,938 / 3.89%

Transcript coverage profile

5' bias: 0.27
3' bias: 0.22
5'-3' bias: 2.04

Junction analysis

Reads at junctions: 25,747,278
ACCT 5.32%
AGGT 4.54%
TCCT 4.2%
ATCT 4.18%
AGGA 3.18%
GCCT 3.03%
CCCT 2.63%
AGCT 2.44%
AGGC 2.33%
TTCT 2.08%
AGAA 1.83%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis