Input data and parameters 

Input

Analysis date: Tue Oct 31 10:04:17 GMT 2023
BAM file: SRX7354351.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): 40,163,752 / 40,122,610
Number of aligned pairs (without duplicates): 40,116,751
Total number of alignments: 84,958,960
Number of secondary alignments: 4,672,598
Number of non-unique alignments: 7,877,302
Aligned to genes: 66,056,398
Ambiguous alignments: 207,353
No feature assigned: 10,555,179
Missing chromosome in annotation: 262,728
Not aligned: 8,409,014

Reads genomic origin

Exonic: 66,056,398 / 86.22%
Intronic: 7,162,990 / 9.35%
Intergenic: 3,392,189 / 4.43%
Intronic/intergenic overlapping exon: 2,691,737 / 3.51%

Transcript coverage profile

5' bias: 0.28
3' bias: 0.17
5'-3' bias: 2.05

Junction analysis

Reads at junctions: 19,948,601
ACCT 5.43%
AGGT 4.66%
ATCT 3.67%
AGGA 3.58%
TCCT 3.36%
GCCT 3.15%
AGCT 2.72%
AGGC 2.39%
AGAT 2.34%
CCCT 2.28%
TTCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis