Input data and parameters 

Input

Analysis date: Sun Oct 29 12:24:05 GMT 2023
BAM file: SRX7354165.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): 46,366,482 / 46,339,236
Number of aligned pairs (without duplicates): 46,334,477
Total number of alignments: 98,372,911
Number of secondary alignments: 5,667,193
Number of non-unique alignments: 9,641,837
Aligned to genes: 75,389,476
Ambiguous alignments: 195,146
No feature assigned: 12,769,900
Missing chromosome in annotation: 376,552
Not aligned: 5,059,886

Reads genomic origin

Exonic: 75,389,476 / 85.51%
Intronic: 7,132,760 / 8.09%
Intergenic: 5,637,140 / 6.39%
Intronic/intergenic overlapping exon: 3,385,638 / 3.84%

Transcript coverage profile

5' bias: 0.25
3' bias: 0.21
5'-3' bias: 2.01

Junction analysis

Reads at junctions: 16,440,295
ACCT 5.14%
AGGT 4.7%
ATCT 3.99%
TCCT 3.71%
AGGA 3.65%
GCCT 2.91%
CCCT 2.63%
AGCT 2.54%
AGGC 2.36%
TTCT 2.24%
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