Input data and parameters 

Input

Analysis date: Tue Oct 31 01:03:44 GMT 2023
BAM file: SRX7354274.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): 23,569,142 / 23,558,672
Number of aligned pairs (without duplicates): 23,555,663
Total number of alignments: 54,185,546
Number of secondary alignments: 7,057,732
Number of non-unique alignments: 9,301,734
Aligned to genes: 33,067,568
Ambiguous alignments: 160,673
No feature assigned: 10,048,298
Missing chromosome in annotation: 1,607,273
Not aligned: 1,368,460

Reads genomic origin

Exonic: 33,067,568 / 76.69%
Intronic: 5,031,996 / 11.67%
Intergenic: 5,016,302 / 11.63%
Intronic/intergenic overlapping exon: 1,551,098 / 3.6%

Transcript coverage profile

5' bias: 0.21
3' bias: 0.23
5'-3' bias: 2.08

Junction analysis

Reads at junctions: 14,157,551
ACCT 4.76%
TCCT 4.62%
AGGT 4.47%
ATCT 3.96%
AGGA 3.08%
CCCT 2.88%
GCCT 2.51%
AGGC 2.31%
AGCT 2.2%
TTCT 2.16%
GTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis