Input data and parameters 

Input

Analysis date: Mon Oct 30 12:49:47 GMT 2023
BAM file: SRX7354234.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): 38,927,039 / 38,897,006
Number of aligned pairs (without duplicates): 38,892,981
Total number of alignments: 82,110,446
Number of secondary alignments: 4,286,401
Number of non-unique alignments: 7,199,834
Aligned to genes: 67,195,445
Ambiguous alignments: 217,100
No feature assigned: 7,211,262
Missing chromosome in annotation: 286,805
Not aligned: 3,915,797

Reads genomic origin

Exonic: 67,195,445 / 90.31%
Intronic: 4,019,375 / 5.4%
Intergenic: 3,191,887 / 4.29%
Intronic/intergenic overlapping exon: 2,723,126 / 3.66%

Transcript coverage profile

5' bias: 0.48
3' bias: 0.16
5'-3' bias: 2.2

Junction analysis

Reads at junctions: 22,465,272
ACCT 5.5%
AGGT 4.78%
AGGA 3.56%
ATCT 3.48%
TCCT 3.39%
GCCT 3.22%
AGCT 2.68%
AGGC 2.46%
AGAT 2.32%
CCCT 2.27%
TTCT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis