Input data and parameters 

Input

Analysis date: Tue Oct 31 15:22:27 GMT 2023
BAM file: SRX7354388.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): 35,521,193 / 35,498,986
Number of aligned pairs (without duplicates): 35,495,677
Total number of alignments: 76,513,013
Number of secondary alignments: 5,492,834
Number of non-unique alignments: 9,115,514
Aligned to genes: 56,459,338
Ambiguous alignments: 217,474
No feature assigned: 10,263,156
Missing chromosome in annotation: 457,531
Not aligned: 2,656,229

Reads genomic origin

Exonic: 56,459,338 / 84.62%
Intronic: 5,405,562 / 8.1%
Intergenic: 4,857,594 / 7.28%
Intronic/intergenic overlapping exon: 2,326,555 / 3.49%

Transcript coverage profile

5' bias: 0.39
3' bias: 0.28
5'-3' bias: 1.75

Junction analysis

Reads at junctions: 22,751,411
ACCT 5.42%
AGGT 4.55%
TCCT 3.9%
ATCT 3.59%
GCCT 3.57%
AGGA 3.23%
CCCT 2.66%
AGCT 2.6%
AGGC 2.44%
TTCT 2.18%
AGAT 2.01%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis