Input data and parameters 

Input

Analysis date: Mon Oct 30 09:26:34 GMT 2023
BAM file: SRX7354134.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): 37,391,266 / 37,365,278
Number of aligned pairs (without duplicates): 37,360,422
Total number of alignments: 79,527,199
Number of secondary alignments: 4,770,655
Number of non-unique alignments: 8,240,486
Aligned to genes: 62,097,508
Ambiguous alignments: 192,412
No feature assigned: 8,730,368
Missing chromosome in annotation: 266,425
Not aligned: 5,957,702

Reads genomic origin

Exonic: 62,097,508 / 87.67%
Intronic: 5,327,260 / 7.52%
Intergenic: 3,403,108 / 4.8%
Intronic/intergenic overlapping exon: 2,426,717 / 3.43%

Transcript coverage profile

5' bias: 0.27
3' bias: 0.17
5'-3' bias: 2.14

Junction analysis

Reads at junctions: 19,049,154
ACCT 5.51%
AGGT 4.75%
AGGA 3.62%
ATCT 3.6%
TCCT 3.34%
GCCT 3.13%
AGCT 2.68%
AGGC 2.39%
CCCT 2.38%
AGAT 2.3%
TTCT 2.17%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis