Input data and parameters 

Input

Analysis date: Mon Oct 30 11:20:41 GMT 2023
BAM file: SRX7354194.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): 35,487,047 / 35,466,496
Number of aligned pairs (without duplicates): 35,463,211
Total number of alignments: 75,429,033
Number of secondary alignments: 4,475,490
Number of non-unique alignments: 7,513,282
Aligned to genes: 60,009,512
Ambiguous alignments: 196,428
No feature assigned: 7,390,473
Missing chromosome in annotation: 319,338
Not aligned: 4,749,257

Reads genomic origin

Exonic: 60,009,512 / 89.03%
Intronic: 4,372,054 / 6.49%
Intergenic: 3,018,419 / 4.48%
Intronic/intergenic overlapping exon: 2,134,930 / 3.17%

Transcript coverage profile

5' bias: 0.32
3' bias: 0.18
5'-3' bias: 2.28

Junction analysis

Reads at junctions: 17,821,940
ACCT 5.44%
AGGT 4.81%
AGGA 3.71%
ATCT 3.66%
TCCT 3.5%
GCCT 2.98%
AGCT 2.71%
AGGC 2.41%
CCCT 2.37%
AGAT 2.35%
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