Input data and parameters 

Input

Analysis date: Tue Oct 31 10:38:48 GMT 2023
BAM file: SRX7354398.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): 42,957,175 / 42,665,456
Number of aligned pairs (without duplicates): 42,627,352
Total number of alignments: 94,883,475
Number of secondary alignments: 9,260,844
Number of non-unique alignments: 12,484,715
Aligned to genes: 61,500,583
Ambiguous alignments: 217,933
No feature assigned: 18,595,463
Missing chromosome in annotation: 2,084,781
Not aligned: 21,937,621

Reads genomic origin

Exonic: 61,500,583 / 76.78%
Intronic: 8,650,594 / 10.8%
Intergenic: 9,944,869 / 12.42%
Intronic/intergenic overlapping exon: 3,573,068 / 4.46%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.24
5'-3' bias: 1.86

Junction analysis

Reads at junctions: 20,779,013
ACCT 5.17%
AGGT 4.7%
TCCT 3.79%
ATCT 3.74%
GCCT 3.42%
AGGA 3.27%
CCCT 2.63%
AGCT 2.61%
TTCT 2.33%
AGGC 2.31%
AGAT 1.95%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis