Input data and parameters 

Input

Analysis date: Mon Oct 30 11:18:12 GMT 2023
BAM file: SRX7354173.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): 46,908,908 / 46,860,329
Number of aligned pairs (without duplicates): 46,830,217
Total number of alignments: 100,016,071
Number of secondary alignments: 6,246,834
Number of non-unique alignments: 10,192,217
Aligned to genes: 78,072,880
Ambiguous alignments: 316,938
No feature assigned: 10,912,637
Missing chromosome in annotation: 521,399
Not aligned: 2,987,145

Reads genomic origin

Exonic: 78,072,880 / 87.74%
Intronic: 7,569,518 / 8.51%
Intergenic: 3,343,119 / 3.76%
Intronic/intergenic overlapping exon: 3,733,646 / 4.2%

Transcript coverage profile

5' bias: 0.46
3' bias: 0.23
5'-3' bias: 1.87

Junction analysis

Reads at junctions: 27,694,468
ACCT 5.04%
AGGT 4.65%
ATCT 3.57%
TCCT 3.51%
AGGA 3.45%
GCCT 3.27%
AGCT 2.81%
CCCT 2.57%
AGGC 2.41%
AGAT 2.14%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis