Input data and parameters 

Input

Analysis date: Sun Oct 29 01:58:18 GMT 2023
BAM file: SRX7354116.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): 62,220,897 / 62,153,948
Number of aligned pairs (without duplicates): 62,128,381
Total number of alignments: 132,928,405
Number of secondary alignments: 8,553,560
Number of non-unique alignments: 14,003,856
Aligned to genes: 102,131,318
Ambiguous alignments: 380,936
No feature assigned: 15,642,160
Missing chromosome in annotation: 770,135
Not aligned: 2,091,043

Reads genomic origin

Exonic: 102,131,318 / 86.72%
Intronic: 11,342,494 / 9.63%
Intergenic: 4,299,666 / 3.65%
Intronic/intergenic overlapping exon: 5,197,728 / 4.41%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.21
5'-3' bias: 1.86

Junction analysis

Reads at junctions: 37,027,422
ACCT 5.33%
AGGT 4.74%
ATCT 3.65%
AGGA 3.54%
TCCT 3.48%
GCCT 3.34%
AGCT 2.64%
CCCT 2.62%
AGGC 2.39%
AGAT 2.26%
TTCT 2.12%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis