Input data and parameters 

Input

Analysis date: Sun Oct 29 01:47:01 GMT 2023
BAM file: SRX7354080.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): 34,002,932 / 33,975,508
Number of aligned pairs (without duplicates): 33,968,964
Total number of alignments: 72,131,249
Number of secondary alignments: 4,152,809
Number of non-unique alignments: 6,944,748
Aligned to genes: 57,037,667
Ambiguous alignments: 177,139
No feature assigned: 7,714,469
Missing chromosome in annotation: 257,226
Not aligned: 6,031,544

Reads genomic origin

Exonic: 57,037,667 / 88.09%
Intronic: 5,294,726 / 8.18%
Intergenic: 2,419,743 / 3.74%
Intronic/intergenic overlapping exon: 2,261,035 / 3.49%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.19
5'-3' bias: 1.79

Junction analysis

Reads at junctions: 18,601,844
ACCT 5.34%
AGGT 4.87%
ATCT 3.82%
TCCT 3.59%
AGGA 3.57%
GCCT 3.07%
AGCT 2.89%
AGGC 2.4%
CCCT 2.23%
AGAT 2.11%
TTCT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis