Input data and parameters 

Input

Analysis date: Mon Oct 30 23:07:05 GMT 2023
BAM file: SRX7354265.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): 50,331,865 / 50,302,897
Number of aligned pairs (without duplicates): 50,295,572
Total number of alignments: 113,335,126
Number of secondary alignments: 12,700,364
Number of non-unique alignments: 15,445,862
Aligned to genes: 81,489,453
Ambiguous alignments: 233,628
No feature assigned: 12,478,984
Missing chromosome in annotation: 3,687,199
Not aligned: 2,699,334

Reads genomic origin

Exonic: 81,489,453 / 86.72%
Intronic: 7,991,507 / 8.5%
Intergenic: 4,487,477 / 4.78%
Intronic/intergenic overlapping exon: 4,026,144 / 4.28%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.13
5'-3' bias: 2.16

Junction analysis

Reads at junctions: 22,937,847
ACCT 5.03%
AGGT 4.58%
AGGA 3.62%
ATCT 3.61%
TCCT 3.35%
GCCT 3%
AGCT 2.83%
TTCT 2.38%
CCCT 2.37%
AGAT 2.3%
AGGC 2.29%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis