Input data and parameters 

Input

Analysis date: Tue Oct 31 10:02:27 GMT 2023
BAM file: SRX7354385.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): 38,480,750 / 38,450,168
Number of aligned pairs (without duplicates): 38,446,171
Total number of alignments: 81,522,038
Number of secondary alignments: 4,591,120
Number of non-unique alignments: 7,599,712
Aligned to genes: 59,675,996
Ambiguous alignments: 215,332
No feature assigned: 13,690,094
Missing chromosome in annotation: 340,904
Not aligned: 4,978,660

Reads genomic origin

Exonic: 59,675,996 / 81.34%
Intronic: 8,587,705 / 11.71%
Intergenic: 5,102,389 / 6.95%
Intronic/intergenic overlapping exon: 2,866,811 / 3.91%

Transcript coverage profile

5' bias: 0.41
3' bias: 0.26
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 22,117,654
ACCT 5.19%
AGGT 4.7%
AGGA 3.48%
ATCT 3.46%
TCCT 3.42%
GCCT 3.31%
AGCT 2.77%
CCCT 2.53%
AGGC 2.41%
AGAT 2.27%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis