Input data and parameters 

Input

Analysis date: Sun Oct 29 01:18:19 GMT 2023
BAM file: SRX7354076.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): 47,851,335 / 47,822,950
Number of aligned pairs (without duplicates): 47,812,514
Total number of alignments: 105,792,541
Number of secondary alignments: 10,118,256
Number of non-unique alignments: 14,817,796
Aligned to genes: 80,687,414
Ambiguous alignments: 397,717
No feature assigned: 8,225,760
Missing chromosome in annotation: 1,663,854
Not aligned: 3,201,471

Reads genomic origin

Exonic: 80,687,414 / 90.75%
Intronic: 4,879,503 / 5.49%
Intergenic: 3,346,257 / 3.76%
Intronic/intergenic overlapping exon: 3,827,583 / 4.3%

Transcript coverage profile

5' bias: 0.06
3' bias: 0.08
5'-3' bias: 2.29

Junction analysis

Reads at junctions: 24,925,098
TCCT 6.55%
ACCT 5.56%
CCCT 5.33%
ATCT 4.79%
AGGT 3.7%
AGGA 2.72%
GTCT 2.41%
AGAC 2.24%
AGGC 2.17%
TCCG 2.11%
GCCT 1.89%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis