Input data and parameters 

Input

Analysis date: Sun Oct 29 11:39:44 GMT 2023
BAM file: SRX7354098.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): 40,954,169 / 40,907,589
Number of aligned pairs (without duplicates): 40,903,546
Total number of alignments: 87,732,681
Number of secondary alignments: 5,870,923
Number of non-unique alignments: 10,179,784
Aligned to genes: 67,926,279
Ambiguous alignments: 225,748
No feature assigned: 9,080,845
Missing chromosome in annotation: 320,025
Not aligned: 6,518,952

Reads genomic origin

Exonic: 67,926,279 / 88.21%
Intronic: 5,496,337 / 7.14%
Intergenic: 3,584,508 / 4.65%
Intronic/intergenic overlapping exon: 2,721,326 / 3.53%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.19
5'-3' bias: 1.97

Junction analysis

Reads at junctions: 20,121,487
ACCT 5.34%
AGGT 4.62%
ATCT 3.64%
AGGA 3.49%
TCCT 3.42%
GCCT 3.35%
AGCT 2.68%
AGGC 2.42%
CCCT 2.39%
AGAT 2.2%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis