Input data and parameters 

Input

Analysis date: Tue Oct 31 09:22:14 GMT 2023
BAM file: SRX7354317.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): 54,016,946 / 53,903,667
Number of aligned pairs (without duplicates): 53,876,686
Total number of alignments: 114,719,360
Number of secondary alignments: 6,798,747
Number of non-unique alignments: 11,461,059
Aligned to genes: 90,728,969
Ambiguous alignments: 315,339
No feature assigned: 11,894,619
Missing chromosome in annotation: 319,374
Not aligned: 11,310,349

Reads genomic origin

Exonic: 90,728,969 / 88.41%
Intronic: 8,004,695 / 7.8%
Intergenic: 3,889,924 / 3.79%
Intronic/intergenic overlapping exon: 4,053,374 / 3.95%

Transcript coverage profile

5' bias: 0.24
3' bias: 0.15
5'-3' bias: 1.78

Junction analysis

Reads at junctions: 28,960,168
ACCT 5.58%
AGGT 4.54%
ATCT 3.88%
TCCT 3.54%
GCCT 3.44%
AGGA 3.28%
AGCT 2.48%
CCCT 2.42%
AGGC 2.28%
TTCT 2.21%
AGAT 2.01%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis