Input data and parameters 

Input

Analysis date: Tue Oct 31 10:31:54 GMT 2023
BAM file: SRX7354360.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): 57,893,283 / 57,820,585
Number of aligned pairs (without duplicates): 57,805,463
Total number of alignments: 124,582,113
Number of secondary alignments: 8,868,245
Number of non-unique alignments: 14,727,861
Aligned to genes: 98,164,991
Ambiguous alignments: 410,652
No feature assigned: 10,618,281
Missing chromosome in annotation: 660,328
Not aligned: 6,784,698

Reads genomic origin

Exonic: 98,164,991 / 90.24%
Intronic: 6,190,393 / 5.69%
Intergenic: 4,427,888 / 4.07%
Intronic/intergenic overlapping exon: 4,275,585 / 3.93%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.19
5'-3' bias: 2

Junction analysis

Reads at junctions: 30,641,264
ACCT 5.32%
ATCT 4.61%
AGGT 4.4%
TCCT 4.3%
GCCT 3.31%
AGGA 3.12%
CCCT 2.93%
AGCT 2.26%
TTCT 2.18%
AGGC 2.15%
AGAA 1.79%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis