Input data and parameters 

Input

Analysis date: Sun Oct 29 02:01:50 GMT 2023
BAM file: SRX7354084.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): 34,617,799 / 34,576,411
Number of aligned pairs (without duplicates): 34,570,775
Total number of alignments: 73,699,286
Number of secondary alignments: 4,505,076
Number of non-unique alignments: 7,243,392
Aligned to genes: 56,955,623
Ambiguous alignments: 175,224
No feature assigned: 8,864,079
Missing chromosome in annotation: 460,968
Not aligned: 6,384,848

Reads genomic origin

Exonic: 56,955,623 / 86.53%
Intronic: 5,356,399 / 8.14%
Intergenic: 3,507,680 / 5.33%
Intronic/intergenic overlapping exon: 2,413,800 / 3.67%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.27
5'-3' bias: 1.61

Junction analysis

Reads at junctions: 21,066,559
ACCT 5.01%
AGGT 5%
TCCT 3.73%
AGGA 3.7%
ATCT 3.64%
AGCT 3.08%
GCCT 2.62%
AGGC 2.51%
CCCT 2.33%
AGAT 2.1%
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