Input data and parameters 

Input

Analysis date: Tue Oct 31 09:43:52 GMT 2023
BAM file: SRX7354299.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): 44,125,859 / 44,088,221
Number of aligned pairs (without duplicates): 44,083,363
Total number of alignments: 93,816,858
Number of secondary alignments: 5,602,778
Number of non-unique alignments: 8,541,249
Aligned to genes: 70,384,529
Ambiguous alignments: 257,424
No feature assigned: 13,836,430
Missing chromosome in annotation: 797,226
Not aligned: 5,094,696

Reads genomic origin

Exonic: 70,384,529 / 83.57%
Intronic: 8,783,178 / 10.43%
Intergenic: 5,053,252 / 6%
Intronic/intergenic overlapping exon: 3,431,241 / 4.07%

Transcript coverage profile

5' bias: 0.51
3' bias: 0.26
5'-3' bias: 1.82

Junction analysis

Reads at junctions: 28,672,667
ACCT 5.32%
AGGT 4.55%
GCCT 3.68%
ATCT 3.53%
TCCT 3.45%
AGGA 3.33%
AGCT 2.79%
CCCT 2.68%
AGGC 2.42%
TTCT 2.3%
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