Input data and parameters 

Input

Analysis date: Mon Oct 30 20:26:34 GMT 2023
BAM file: SRX7354206.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): 48,798,369 / 48,759,299
Number of aligned pairs (without duplicates): 48,753,247
Total number of alignments: 103,147,508
Number of secondary alignments: 5,589,840
Number of non-unique alignments: 9,139,498
Aligned to genes: 81,187,506
Ambiguous alignments: 236,505
No feature assigned: 12,088,249
Missing chromosome in annotation: 495,750
Not aligned: 5,523,314

Reads genomic origin

Exonic: 81,187,506 / 87.04%
Intronic: 7,517,512 / 8.06%
Intergenic: 4,570,737 / 4.9%
Intronic/intergenic overlapping exon: 3,503,395 / 3.76%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.16
5'-3' bias: 1.97

Junction analysis

Reads at junctions: 24,540,697
ACCT 5.41%
AGGT 4.95%
AGGA 3.73%
ATCT 3.62%
TCCT 3.47%
GCCT 2.96%
AGCT 2.74%
AGGC 2.5%
CCCT 2.37%
AGAT 2.33%
TTCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis