Input data and parameters 

Input

Analysis date: Sun Oct 29 01:49:46 GMT 2023
BAM file: SRX7354107.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): 48,135,034 / 48,096,378
Number of aligned pairs (without duplicates): 48,089,477
Total number of alignments: 102,371,307
Number of secondary alignments: 6,139,895
Number of non-unique alignments: 10,105,013
Aligned to genes: 81,728,412
Ambiguous alignments: 258,134
No feature assigned: 9,824,937
Missing chromosome in annotation: 454,811
Not aligned: 7,546,390

Reads genomic origin

Exonic: 81,728,412 / 89.27%
Intronic: 6,242,147 / 6.82%
Intergenic: 3,582,790 / 3.91%
Intronic/intergenic overlapping exon: 3,182,545 / 3.48%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.18
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 25,396,010
ACCT 5.16%
AGGT 4.89%
ATCT 3.78%
AGGA 3.55%
TCCT 3.47%
GCCT 2.91%
AGCT 2.75%
AGGC 2.51%
CCCT 2.38%
AGAT 2.12%
TTCT 2.06%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis