Input data and parameters 

Input

Analysis date: Tue Oct 31 09:33:29 GMT 2023
BAM file: SRX7354296.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): 39,150,823 / 39,128,565
Number of aligned pairs (without duplicates): 39,124,975
Total number of alignments: 83,265,369
Number of secondary alignments: 4,985,981
Number of non-unique alignments: 8,532,303
Aligned to genes: 66,420,878
Ambiguous alignments: 213,951
No feature assigned: 7,810,287
Missing chromosome in annotation: 287,950
Not aligned: 2,608,366

Reads genomic origin

Exonic: 66,420,878 / 89.48%
Intronic: 4,887,428 / 6.58%
Intergenic: 2,922,859 / 3.94%
Intronic/intergenic overlapping exon: 2,426,467 / 3.27%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.19
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 20,003,816
ACCT 5.35%
AGGT 4.57%
ATCT 3.68%
AGGA 3.5%
TCCT 3.32%
GCCT 3.27%
AGCT 2.74%
CCCT 2.37%
AGGC 2.33%
AGAT 2.22%
TTCT 2.18%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis