Input data and parameters 

Input

Analysis date: Tue Oct 31 09:52:00 GMT 2023
BAM file: SRX7354330.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): 44,876,832 / 44,805,443
Number of aligned pairs (without duplicates): 44,797,715
Total number of alignments: 95,887,429
Number of secondary alignments: 6,205,154
Number of non-unique alignments: 9,616,604
Aligned to genes: 73,211,538
Ambiguous alignments: 261,017
No feature assigned: 12,007,032
Missing chromosome in annotation: 791,238
Not aligned: 14,309,273

Reads genomic origin

Exonic: 73,211,538 / 85.91%
Intronic: 7,214,591 / 8.47%
Intergenic: 4,792,441 / 5.62%
Intronic/intergenic overlapping exon: 3,276,302 / 3.84%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.29
5'-3' bias: 1.74

Junction analysis

Reads at junctions: 26,028,734
ACCT 5.18%
AGGT 4.77%
TCCT 3.66%
ATCT 3.65%
AGGA 3.47%
GCCT 3.01%
AGCT 2.75%
CCCT 2.63%
AGGC 2.43%
TTCT 2.14%
AGAT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis