Input data and parameters 

Input

Analysis date: Tue Oct 31 09:48:08 GMT 2023
BAM file: SRX7354367.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): 36,812,997 / 36,790,647
Number of aligned pairs (without duplicates): 36,787,653
Total number of alignments: 77,810,803
Number of secondary alignments: 4,207,159
Number of non-unique alignments: 7,156,647
Aligned to genes: 62,278,552
Ambiguous alignments: 191,211
No feature assigned: 7,932,149
Missing chromosome in annotation: 252,244
Not aligned: 3,510,024

Reads genomic origin

Exonic: 62,278,552 / 88.7%
Intronic: 4,993,491 / 7.11%
Intergenic: 2,938,658 / 4.19%
Intronic/intergenic overlapping exon: 2,293,994 / 3.27%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.16
5'-3' bias: 2.12

Junction analysis

Reads at junctions: 18,914,375
ACCT 5.43%
AGGT 4.69%
ATCT 3.7%
AGGA 3.56%
TCCT 3.37%
GCCT 3.34%
AGCT 2.71%
AGGC 2.34%
AGAT 2.29%
CCCT 2.27%
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