Input data and parameters 

Input

Analysis date: Sun Oct 29 02:09:33 GMT 2023
BAM file: SRX7354097.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): 73,092,226 / 73,052,131
Number of aligned pairs (without duplicates): 73,036,537
Total number of alignments: 158,509,928
Number of secondary alignments: 12,365,571
Number of non-unique alignments: 19,498,233
Aligned to genes: 125,137,379
Ambiguous alignments: 555,416
No feature assigned: 11,929,206
Missing chromosome in annotation: 1,389,694
Not aligned: 5,120,351

Reads genomic origin

Exonic: 125,137,379 / 91.3%
Intronic: 6,781,220 / 4.95%
Intergenic: 5,147,986 / 3.76%
Intronic/intergenic overlapping exon: 5,820,628 / 4.25%

Transcript coverage profile

5' bias: 0.1
3' bias: 0.12
5'-3' bias: 1.94

Junction analysis

Reads at junctions: 43,410,114
ACCT 5.2%
TCCT 5.03%
ATCT 4.59%
AGGT 4.37%
CCCT 3.51%
AGGA 2.88%
GCCT 2.41%
AGGC 2.35%
TTCT 2.28%
AGCT 1.97%
AGAC 1.87%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis