Input data and parameters 

Input

Analysis date: Tue Oct 31 10:04:30 GMT 2023
BAM file: SRX7354390.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): 40,458,251 / 40,410,282
Number of aligned pairs (without duplicates): 40,404,029
Total number of alignments: 85,794,485
Number of secondary alignments: 4,925,952
Number of non-unique alignments: 8,237,868
Aligned to genes: 67,759,453
Ambiguous alignments: 245,849
No feature assigned: 9,227,744
Missing chromosome in annotation: 323,571
Not aligned: 9,399,283

Reads genomic origin

Exonic: 67,759,453 / 88.01%
Intronic: 5,797,112 / 7.53%
Intergenic: 3,430,632 / 4.46%
Intronic/intergenic overlapping exon: 2,845,314 / 3.7%

Transcript coverage profile

5' bias: 0.35
3' bias: 0.21
5'-3' bias: 1.8

Junction analysis

Reads at junctions: 22,723,999
ACCT 5.43%
AGGT 4.59%
ATCT 3.5%
AGGA 3.43%
TCCT 3.43%
GCCT 3.36%
AGCT 2.75%
CCCT 2.43%
AGGC 2.4%
AGAT 2.29%
TTCT 2.15%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis