Input data and parameters 

Input

Analysis date: Tue Oct 31 01:22:45 GMT 2023
BAM file: SRX7354368.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): 37,170,428 / 37,141,768
Number of aligned pairs (without duplicates): 37,136,460
Total number of alignments: 79,811,499
Number of secondary alignments: 5,499,303
Number of non-unique alignments: 8,850,688
Aligned to genes: 59,896,902
Ambiguous alignments: 241,323
No feature assigned: 10,393,799
Missing chromosome in annotation: 428,787
Not aligned: 3,059,134

Reads genomic origin

Exonic: 59,896,902 / 85.21%
Intronic: 7,411,119 / 10.54%
Intergenic: 2,982,680 / 4.24%
Intronic/intergenic overlapping exon: 2,348,760 / 3.34%

Transcript coverage profile

5' bias: 0.5
3' bias: 0.23
5'-3' bias: 1.96

Junction analysis

Reads at junctions: 21,483,991
ACCT 5.37%
AGGT 4.65%
AGGA 3.53%
ATCT 3.51%
TCCT 3.41%
GCCT 2.8%
AGCT 2.75%
TTCT 2.4%
CCCT 2.37%
AGGC 2.35%
AGAT 2.34%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis