Input data and parameters 

Input

Analysis date: Tue Oct 31 09:19:50 GMT 2023
BAM file: SRX7354318.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): 52,502,071 / 52,458,507
Number of aligned pairs (without duplicates): 52,441,709
Total number of alignments: 115,565,285
Number of secondary alignments: 10,604,707
Number of non-unique alignments: 16,821,063
Aligned to genes: 88,349,820
Ambiguous alignments: 386,456
No feature assigned: 8,902,341
Missing chromosome in annotation: 1,105,605
Not aligned: 3,468,956

Reads genomic origin

Exonic: 88,349,820 / 90.85%
Intronic: 4,775,809 / 4.91%
Intergenic: 4,126,532 / 4.24%
Intronic/intergenic overlapping exon: 3,990,766 / 4.1%

Transcript coverage profile

5' bias: 0.08
3' bias: 0.12
5'-3' bias: 2.02

Junction analysis

Reads at junctions: 29,041,321
TCCT 6.42%
ACCT 5.13%
ATCT 4.69%
AGGT 3.96%
CCCT 3.88%
AGGA 2.76%
GCCT 2.33%
GTCT 2.24%
AGGC 2.23%
TTCT 2.18%
TCCC 2.07%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis