Input data and parameters 

Input

Analysis date: Tue Oct 31 10:02:25 GMT 2023
BAM file: SRX7354379.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): 45,605,018 / 45,578,202
Number of aligned pairs (without duplicates): 45,557,191
Total number of alignments: 98,959,164
Number of secondary alignments: 7,775,944
Number of non-unique alignments: 12,968,935
Aligned to genes: 75,062,036
Ambiguous alignments: 307,213
No feature assigned: 10,022,293
Missing chromosome in annotation: 598,687
Not aligned: 2,084,512

Reads genomic origin

Exonic: 75,062,036 / 88.22%
Intronic: 6,511,748 / 7.65%
Intergenic: 3,510,545 / 4.13%
Intronic/intergenic overlapping exon: 3,710,751 / 4.36%

Transcript coverage profile

5' bias: 0.42
3' bias: 0.23
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 27,115,102
ACCT 5.34%
AGGT 4.51%
TCCT 3.95%
ATCT 3.88%
GCCT 3.53%
AGGA 3.19%
CCCT 2.92%
AGCT 2.56%
AGGC 2.38%
TTCT 2.12%
AGAT 1.84%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis