Input data and parameters 

Input

Analysis date: Mon Oct 30 20:41:15 GMT 2023
BAM file: SRX7354227.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): 44,364,195 / 44,321,425
Number of aligned pairs (without duplicates): 44,293,687
Total number of alignments: 94,419,504
Number of secondary alignments: 5,733,884
Number of non-unique alignments: 9,332,957
Aligned to genes: 74,640,944
Ambiguous alignments: 238,138
No feature assigned: 9,787,525
Missing chromosome in annotation: 419,940
Not aligned: 1,856,844

Reads genomic origin

Exonic: 74,640,944 / 88.41%
Intronic: 7,425,120 / 8.79%
Intergenic: 2,362,405 / 2.8%
Intronic/intergenic overlapping exon: 3,699,958 / 4.38%

Transcript coverage profile

5' bias: 0.51
3' bias: 0.19
5'-3' bias: 1.97

Junction analysis

Reads at junctions: 30,034,015
AGGT 4.91%
ACCT 4.68%
ATCT 4.02%
TCCT 3.76%
AGGA 3.69%
AGCT 3.23%
GCCT 2.72%
CCCT 2.44%
AGGC 2.4%
AGAT 2.03%
AGGG 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis