Input data and parameters 

Input

Analysis date: Sun Oct 29 01:22:36 GMT 2023
BAM file: SRX7354071.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): 43,894,751 / 43,874,614
Number of aligned pairs (without duplicates): 43,867,255
Total number of alignments: 96,740,860
Number of secondary alignments: 8,971,495
Number of non-unique alignments: 13,305,514
Aligned to genes: 74,123,370
Ambiguous alignments: 322,227
No feature assigned: 7,631,213
Missing chromosome in annotation: 1,358,536
Not aligned: 2,457,257

Reads genomic origin

Exonic: 74,123,370 / 90.67%
Intronic: 4,404,924 / 5.39%
Intergenic: 3,226,289 / 3.95%
Intronic/intergenic overlapping exon: 3,787,784 / 4.63%

Transcript coverage profile

5' bias: 0.11
3' bias: 0.13
5'-3' bias: 2.24

Junction analysis

Reads at junctions: 26,142,734
TCCT 5.54%
ACCT 5.18%
ATCT 4.42%
AGGT 4.2%
CCCT 3.37%
AGGA 3.01%
GCCT 2.36%
AGGC 2.25%
TTCT 2.18%
TCCC 1.96%
AGCT 1.91%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis