Input data and parameters 

Input

Analysis date: Mon Oct 30 20:30:11 GMT 2023
BAM file: SRX7354257.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): 37,371,332 / 37,350,980
Number of aligned pairs (without duplicates): 37,347,737
Total number of alignments: 79,305,212
Number of secondary alignments: 4,582,900
Number of non-unique alignments: 6,988,597
Aligned to genes: 60,971,233
Ambiguous alignments: 197,631
No feature assigned: 10,487,770
Missing chromosome in annotation: 659,981
Not aligned: 1,455,100

Reads genomic origin

Exonic: 60,971,233 / 85.32%
Intronic: 6,599,593 / 9.24%
Intergenic: 3,888,177 / 5.44%
Intronic/intergenic overlapping exon: 2,936,962 / 4.11%

Transcript coverage profile

5' bias: 0.49
3' bias: 0.25
5'-3' bias: 1.89

Junction analysis

Reads at junctions: 23,168,261
ACCT 5.31%
AGGT 4.68%
TCCT 3.68%
ATCT 3.57%
AGGA 3.37%
GCCT 3.3%
AGCT 2.74%
CCCT 2.62%
AGGC 2.45%
TTCT 2.27%
AGAT 2.19%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis