Input data and parameters 

Input

Analysis date: Tue Oct 31 16:15:17 GMT 2023
BAM file: SRX7354389.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): 51,309,619 / 51,280,118
Number of aligned pairs (without duplicates): 51,246,964
Total number of alignments: 109,799,601
Number of secondary alignments: 7,209,864
Number of non-unique alignments: 12,063,631
Aligned to genes: 86,784,590
Ambiguous alignments: 424,955
No feature assigned: 10,142,573
Missing chromosome in annotation: 383,852
Not aligned: 1,963,701

Reads genomic origin

Exonic: 86,784,590 / 89.54%
Intronic: 6,592,713 / 6.8%
Intergenic: 3,549,860 / 3.66%
Intronic/intergenic overlapping exon: 4,623,846 / 4.77%

Transcript coverage profile

5' bias: 0.23
3' bias: 0.19
5'-3' bias: 1.73

Junction analysis

Reads at junctions: 33,614,555
ACCT 5.18%
TCCT 4.84%
ATCT 4.76%
AGGT 4.21%
CCCT 3.36%
GCCT 3.19%
AGGA 2.91%
TTCT 2.36%
AGGC 2.3%
AGCT 2.16%
GTCT 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis