Input data and parameters 

Input

Analysis date: Sun Oct 29 01:40:14 GMT 2023
BAM file: SRX7354113.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): 37,921,046 / 37,905,083
Number of aligned pairs (without duplicates): 37,901,715
Total number of alignments: 80,826,523
Number of secondary alignments: 5,000,394
Number of non-unique alignments: 7,909,621
Aligned to genes: 63,052,001
Ambiguous alignments: 210,791
No feature assigned: 9,131,213
Missing chromosome in annotation: 522,897
Not aligned: 1,786,247

Reads genomic origin

Exonic: 63,052,001 / 87.35%
Intronic: 6,706,362 / 9.29%
Intergenic: 2,424,851 / 3.36%
Intronic/intergenic overlapping exon: 2,277,998 / 3.16%

Transcript coverage profile

5' bias: 0.46
3' bias: 0.19
5'-3' bias: 2.09

Junction analysis

Reads at junctions: 21,316,452
ACCT 5.58%
AGGT 4.68%
ATCT 3.51%
AGGA 3.46%
TCCT 3.22%
GCCT 3.22%
AGCT 2.79%
CCCT 2.45%
AGGC 2.41%
AGAT 2.36%
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