Input data and parameters 

Input

Analysis date: Tue Oct 31 09:28:02 GMT 2023
BAM file: SRX7354326.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): 29,093,064 / 29,065,975
Number of aligned pairs (without duplicates): 29,059,926
Total number of alignments: 61,777,241
Number of secondary alignments: 3,618,202
Number of non-unique alignments: 6,036,853
Aligned to genes: 50,491,752
Ambiguous alignments: 176,781
No feature assigned: 4,842,072
Missing chromosome in annotation: 229,783
Not aligned: 3,994,057

Reads genomic origin

Exonic: 50,491,752 / 91.25%
Intronic: 2,819,118 / 5.09%
Intergenic: 2,022,954 / 3.66%
Intronic/intergenic overlapping exon: 1,790,650 / 3.24%

Transcript coverage profile

5' bias: 0.18
3' bias: 0.17
5'-3' bias: 1.99

Junction analysis

Reads at junctions: 14,935,348
ACCT 5.44%
AGGT 4.69%
ATCT 4.51%
TCCT 3.98%
GCCT 3.17%
AGGA 3.14%
CCCT 3.01%
TTCT 2.28%
AGGC 2.21%
AGCT 2.16%
AGAA 1.99%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis