Input data and parameters 

Input

Analysis date: Tue Oct 31 09:54:29 GMT 2023
BAM file: SRX7354357.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): 34,524,482 / 34,500,902
Number of aligned pairs (without duplicates): 34,497,837
Total number of alignments: 73,362,690
Number of secondary alignments: 4,337,306
Number of non-unique alignments: 7,289,346
Aligned to genes: 58,226,690
Ambiguous alignments: 206,409
No feature assigned: 7,407,042
Missing chromosome in annotation: 233,203
Not aligned: 3,289,952

Reads genomic origin

Exonic: 58,226,690 / 88.71%
Intronic: 5,314,185 / 8.1%
Intergenic: 2,092,857 / 3.19%
Intronic/intergenic overlapping exon: 2,015,350 / 3.07%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.16
5'-3' bias: 2.05

Junction analysis

Reads at junctions: 19,632,082
ACCT 5.34%
AGGT 4.69%
ATCT 3.64%
AGGA 3.57%
TCCT 3.44%
GCCT 3.1%
AGCT 2.79%
AGGC 2.33%
AGAT 2.29%
CCCT 2.27%
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