Input data and parameters 

Input

Analysis date: Sun Oct 29 02:05:52 GMT 2023
BAM file: SRX7354124.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): 43,818,274 / 43,756,651
Number of aligned pairs (without duplicates): 43,741,720
Total number of alignments: 92,685,714
Number of secondary alignments: 5,110,789
Number of non-unique alignments: 8,643,914
Aligned to genes: 71,345,121
Ambiguous alignments: 204,702
No feature assigned: 12,174,338
Missing chromosome in annotation: 317,639
Not aligned: 7,222,245

Reads genomic origin

Exonic: 71,345,121 / 85.42%
Intronic: 8,445,716 / 10.11%
Intergenic: 3,728,622 / 4.46%
Intronic/intergenic overlapping exon: 3,524,589 / 4.22%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.14
5'-3' bias: 2.15

Junction analysis

Reads at junctions: 22,817,979
ACCT 5.36%
AGGT 4.68%
AGGA 3.69%
ATCT 3.63%
TCCT 3.38%
GCCT 2.93%
AGCT 2.71%
AGAT 2.4%
AGGC 2.33%
CCCT 2.23%
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