Input data and parameters 

Input

Analysis date: Sun Oct 29 01:31:06 GMT 2023
BAM file: SRX7354083.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): 30,485,767 / 30,467,542
Number of aligned pairs (without duplicates): 30,464,423
Total number of alignments: 64,636,701
Number of secondary alignments: 3,683,392
Number of non-unique alignments: 6,035,287
Aligned to genes: 52,458,795
Ambiguous alignments: 189,767
No feature assigned: 5,669,561
Missing chromosome in annotation: 283,291
Not aligned: 2,290,827

Reads genomic origin

Exonic: 52,458,795 / 90.25%
Intronic: 3,783,219 / 6.51%
Intergenic: 1,886,342 / 3.25%
Intronic/intergenic overlapping exon: 2,060,500 / 3.54%

Transcript coverage profile

5' bias: 0.29
3' bias: 0.19
5'-3' bias: 1.88

Junction analysis

Reads at junctions: 16,760,098
ACCT 5.44%
AGGT 4.68%
ATCT 3.94%
TCCT 3.64%
AGGA 3.23%
GCCT 3.15%
AGCT 2.52%
TTCT 2.47%
CCCT 2.47%
AGGC 2.36%
AGAT 1.97%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis