Input data and parameters 

Input

Analysis date: Sun Oct 29 02:01:34 GMT 2023
BAM file: SRX7354126.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): 51,731,630 / 51,676,716
Number of aligned pairs (without duplicates): 51,656,280
Total number of alignments: 114,520,880
Number of secondary alignments: 11,112,534
Number of non-unique alignments: 14,284,182
Aligned to genes: 85,322,404
Ambiguous alignments: 262,254
No feature assigned: 11,895,006
Missing chromosome in annotation: 2,757,034
Not aligned: 2,441,810

Reads genomic origin

Exonic: 85,322,404 / 87.76%
Intronic: 8,234,434 / 8.47%
Intergenic: 3,660,572 / 3.77%
Intronic/intergenic overlapping exon: 3,855,580 / 3.97%

Transcript coverage profile

5' bias: 0.47
3' bias: 0.22
5'-3' bias: 1.73

Junction analysis

Reads at junctions: 28,099,849
ACCT 4.88%
AGGT 4.83%
ATCT 3.66%
AGGA 3.59%
TCCT 3.58%
GCCT 3.09%
AGCT 3.01%
CCCT 2.59%
AGGC 2.41%
TTCT 2.14%
AGAT 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