Input data and parameters 

Input

Analysis date: Tue Oct 31 09:50:26 GMT 2023
BAM file: SRX7354352.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): 44,298,364 / 44,234,181
Number of aligned pairs (without duplicates): 44,223,683
Total number of alignments: 95,914,859
Number of secondary alignments: 7,382,314
Number of non-unique alignments: 12,667,803
Aligned to genes: 73,658,809
Ambiguous alignments: 287,580
No feature assigned: 8,925,165
Missing chromosome in annotation: 375,502
Not aligned: 3,816,697

Reads genomic origin

Exonic: 73,658,809 / 89.19%
Intronic: 5,536,302 / 6.7%
Intergenic: 3,388,863 / 4.1%
Intronic/intergenic overlapping exon: 3,360,899 / 4.07%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.23
5'-3' bias: 1.78

Junction analysis

Reads at junctions: 22,470,791
ACCT 5.17%
AGGT 4.54%
TCCT 4.04%
ATCT 3.93%
GCCT 3.35%
AGGA 3.26%
CCCT 2.84%
AGCT 2.49%
AGGC 2.34%
TTCT 2.21%
AGAT 1.86%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis