Input data and parameters 

Input

Analysis date: Mon Oct 30 22:57:49 GMT 2023
BAM file: SRX7354261.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): 46,467,889 / 46,415,739
Number of aligned pairs (without duplicates): 46,391,186
Total number of alignments: 99,528,063
Number of secondary alignments: 6,644,435
Number of non-unique alignments: 10,313,707
Aligned to genes: 78,071,355
Ambiguous alignments: 385,191
No feature assigned: 9,970,882
Missing chromosome in annotation: 786,928
Not aligned: 2,447,362

Reads genomic origin

Exonic: 78,071,355 / 88.67%
Intronic: 6,463,156 / 7.34%
Intergenic: 3,507,726 / 3.98%
Intronic/intergenic overlapping exon: 4,719,965 / 5.36%

Transcript coverage profile

5' bias: 0.25
3' bias: 0.19
5'-3' bias: 1.95

Junction analysis

Reads at junctions: 28,142,784
ACCT 5.52%
TCCT 5.13%
ATCT 4.53%
AGGT 4.16%
CCCT 3.29%
GCCT 3.18%
AGGA 2.91%
TTCT 2.36%
AGGC 2.22%
GTCT 2.13%
AGCT 2.08%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis