Input data and parameters 

Input

Analysis date: Sun Oct 29 01:20:50 GMT 2023
BAM file: SRX7354105.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): 50,061,270 / 50,020,465
Number of aligned pairs (without duplicates): 50,012,580
Total number of alignments: 106,422,720
Number of secondary alignments: 6,340,985
Number of non-unique alignments: 10,505,566
Aligned to genes: 84,025,171
Ambiguous alignments: 259,803
No feature assigned: 11,163,723
Missing chromosome in annotation: 468,457
Not aligned: 8,516,585

Reads genomic origin

Exonic: 84,025,171 / 88.27%
Intronic: 6,685,446 / 7.02%
Intergenic: 4,478,277 / 4.7%
Intronic/intergenic overlapping exon: 3,323,879 / 3.49%

Transcript coverage profile

5' bias: 0.26
3' bias: 0.12
5'-3' bias: 2.3

Junction analysis

Reads at junctions: 27,747,968
ACCT 5.55%
AGGT 4.65%
ATCT 3.63%
AGGA 3.61%
TCCT 3.33%
GCCT 3.22%
AGCT 2.62%
AGGC 2.37%
CCCT 2.27%
AGAT 2.25%
TTCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis