Input data and parameters 

Input

Analysis date: Mon Oct 30 20:00:07 GMT 2023
BAM file: SRX7354238.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): 27,802,942 / 27,787,881
Number of aligned pairs (without duplicates): 27,785,923
Total number of alignments: 59,008,272
Number of secondary alignments: 3,417,449
Number of non-unique alignments: 5,663,668
Aligned to genes: 47,674,732
Ambiguous alignments: 168,739
No feature assigned: 5,248,034
Missing chromosome in annotation: 253,099
Not aligned: 3,010,313

Reads genomic origin

Exonic: 47,674,732 / 90.08%
Intronic: 3,351,826 / 6.33%
Intergenic: 1,896,208 / 3.58%
Intronic/intergenic overlapping exon: 1,579,212 / 2.98%

Transcript coverage profile

5' bias: 0.3
3' bias: 0.17
5'-3' bias: 2.01

Junction analysis

Reads at junctions: 15,769,843
ACCT 5.54%
AGGT 4.59%
ATCT 3.58%
AGGA 3.49%
GCCT 3.43%
TCCT 3.42%
AGCT 2.67%
AGGC 2.32%
CCCT 2.28%
AGAT 2.21%
TTCT 2.2%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis