Input data and parameters 

Input

Analysis date: Tue Oct 31 10:24:49 GMT 2023
BAM file: SRX7354349.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): 45,068,723 / 44,952,878
Number of aligned pairs (without duplicates): 44,934,915
Total number of alignments: 96,660,658
Number of secondary alignments: 6,639,057
Number of non-unique alignments: 10,940,999
Aligned to genes: 72,602,270
Ambiguous alignments: 284,043
No feature assigned: 12,589,307
Missing chromosome in annotation: 244,039
Not aligned: 7,240,043

Reads genomic origin

Exonic: 72,602,270 / 85.22%
Intronic: 10,527,468 / 12.36%
Intergenic: 2,061,839 / 2.42%
Intronic/intergenic overlapping exon: 3,610,128 / 4.24%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.17
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 28,092,943
ACCT 5.8%
AGGT 4.78%
TCCT 3.76%
AGGA 3.76%
ATCT 3.45%
AGCT 2.68%
AGAT 2.42%
TTCT 2.28%
GCCT 2.26%
AGGC 2.24%
CCCT 2.22%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis