Input data and parameters 

Input

Analysis date: Tue Oct 31 17:22:57 GMT 2023
BAM file: SRX7354399.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): 34,397,778 / 34,367,993
Number of aligned pairs (without duplicates): 34,364,255
Total number of alignments: 73,559,242
Number of secondary alignments: 4,793,471
Number of non-unique alignments: 7,789,852
Aligned to genes: 56,554,545
Ambiguous alignments: 201,027
No feature assigned: 8,622,371
Missing chromosome in annotation: 391,447
Not aligned: 3,216,021

Reads genomic origin

Exonic: 56,554,545 / 86.77%
Intronic: 5,942,717 / 9.12%
Intergenic: 2,679,654 / 4.11%
Intronic/intergenic overlapping exon: 2,017,978 / 3.1%

Transcript coverage profile

5' bias: 0.44
3' bias: 0.21
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 18,641,697
ACCT 5.3%
AGGT 4.65%
ATCT 3.57%
AGGA 3.51%
TCCT 3.4%
GCCT 3.14%
AGCT 2.76%
TTCT 2.59%
CCCT 2.38%
AGGC 2.31%
AGAT 2.25%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis