Input data and parameters 

Input

Analysis date: Sun Oct 29 13:07:22 GMT 2023
BAM file: SRX7354151.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): 39,209,076 / 39,176,786
Number of aligned pairs (without duplicates): 39,170,967
Total number of alignments: 82,782,493
Number of secondary alignments: 4,396,631
Number of non-unique alignments: 7,375,215
Aligned to genes: 64,308,824
Ambiguous alignments: 220,081
No feature assigned: 10,587,762
Missing chromosome in annotation: 290,611
Not aligned: 7,731,602

Reads genomic origin

Exonic: 64,308,824 / 85.86%
Intronic: 7,313,756 / 9.77%
Intergenic: 3,274,006 / 4.37%
Intronic/intergenic overlapping exon: 2,881,661 / 3.85%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.2
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 21,977,265
ACCT 5.26%
AGGT 4.65%
ATCT 3.73%
AGGA 3.55%
TCCT 3.36%
GCCT 3.12%
AGCT 2.78%
AGGC 2.41%
AGAT 2.33%
CCCT 2.33%
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