Input data and parameters 

Input

Analysis date: Tue Oct 31 17:45:45 GMT 2023
BAM file: SRX7354409.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): 56,903,112 / 56,866,497
Number of aligned pairs (without duplicates): 56,861,803
Total number of alignments: 122,002,576
Number of secondary alignments: 8,232,967
Number of non-unique alignments: 12,661,324
Aligned to genes: 88,121,710
Ambiguous alignments: 345,631
No feature assigned: 19,886,966
Missing chromosome in annotation: 986,945
Not aligned: 4,511,863

Reads genomic origin

Exonic: 88,121,710 / 81.59%
Intronic: 13,946,910 / 12.91%
Intergenic: 5,940,056 / 5.5%
Intronic/intergenic overlapping exon: 3,942,835 / 3.65%

Transcript coverage profile

5' bias: 0.53
3' bias: 0.33
5'-3' bias: 1.65

Junction analysis

Reads at junctions: 36,835,913
ACCT 5.21%
AGGT 4.66%
TCCT 3.53%
AGGA 3.41%
GCCT 3.36%
ATCT 3.35%
AGCT 2.8%
CCCT 2.59%
AGGC 2.46%
AGAT 2.18%
TTCT 2.09%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis