Input data and parameters 

Input

Analysis date: Tue Oct 31 09:30:07 GMT 2023
BAM file: SRX7354335.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): 51,932,319 / 51,881,634
Number of aligned pairs (without duplicates): 51,874,937
Total number of alignments: 111,146,297
Number of secondary alignments: 7,332,344
Number of non-unique alignments: 12,347,491
Aligned to genes: 87,599,963
Ambiguous alignments: 306,042
No feature assigned: 10,429,478
Missing chromosome in annotation: 463,323
Not aligned: 14,904,677

Reads genomic origin

Exonic: 87,599,963 / 89.36%
Intronic: 6,161,620 / 6.29%
Intergenic: 4,267,858 / 4.35%
Intronic/intergenic overlapping exon: 2,934,142 / 2.99%

Transcript coverage profile

5' bias: 0.33
3' bias: 0.19
5'-3' bias: 2.21

Junction analysis

Reads at junctions: 25,377,641
ACCT 5.51%
AGGT 4.8%
ATCT 3.73%
TCCT 3.59%
AGGA 3.52%
GCCT 3.17%
CCCT 2.72%
AGCT 2.52%
AGGC 2.37%
TTCT 2.29%
AGAT 2.23%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis