Input data and parameters 

Input

Analysis date: Mon Oct 30 20:28:59 GMT 2023
BAM file: SRX7354232.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): 40,554,348 / 40,507,349
Number of aligned pairs (without duplicates): 40,499,637
Total number of alignments: 85,777,893
Number of secondary alignments: 4,716,196
Number of non-unique alignments: 7,866,944
Aligned to genes: 69,075,639
Ambiguous alignments: 261,942
No feature assigned: 8,254,420
Missing chromosome in annotation: 318,948
Not aligned: 6,272,243

Reads genomic origin

Exonic: 69,075,639 / 89.33%
Intronic: 4,862,558 / 6.29%
Intergenic: 3,391,862 / 4.39%
Intronic/intergenic overlapping exon: 2,897,339 / 3.75%

Transcript coverage profile

5' bias: 0.36
3' bias: 0.19
5'-3' bias: 1.83

Junction analysis

Reads at junctions: 22,012,731
ACCT 5.52%
AGGT 4.71%
ATCT 3.89%
TCCT 3.66%
GCCT 3.44%
AGGA 3.4%
CCCT 2.55%
AGCT 2.49%
AGGC 2.4%
TTCT 2.27%
AGAT 2.1%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis