Input data and parameters 

Input

Analysis date: Tue Oct 31 09:59:15 GMT 2023
BAM file: SRX7354319.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): 49,041,933 / 48,986,119
Number of aligned pairs (without duplicates): 48,978,285
Total number of alignments: 104,078,901
Number of secondary alignments: 6,050,849
Number of non-unique alignments: 10,244,468
Aligned to genes: 79,897,812
Ambiguous alignments: 251,771
No feature assigned: 13,335,464
Missing chromosome in annotation: 349,386
Not aligned: 9,068,550

Reads genomic origin

Exonic: 79,897,812 / 85.7%
Intronic: 8,661,107 / 9.29%
Intergenic: 4,674,357 / 5.01%
Intronic/intergenic overlapping exon: 3,459,083 / 3.71%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.13
5'-3' bias: 2.4

Junction analysis

Reads at junctions: 23,721,100
ACCT 5.39%
AGGT 4.76%
AGGA 3.75%
TCCT 3.54%
ATCT 3.52%
GCCT 2.91%
AGCT 2.71%
AGAT 2.38%
AGGC 2.33%
CCCT 2.27%
TTCT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis