Input data and parameters 

Input

Analysis date: Tue Oct 31 09:07:12 GMT 2023
BAM file: SRX7354304.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): 36,151,874 / 36,130,923
Number of aligned pairs (without duplicates): 36,126,973
Total number of alignments: 76,902,887
Number of secondary alignments: 4,620,090
Number of non-unique alignments: 7,351,077
Aligned to genes: 60,816,070
Ambiguous alignments: 238,108
No feature assigned: 8,062,820
Missing chromosome in annotation: 434,812
Not aligned: 3,374,095

Reads genomic origin

Exonic: 60,816,070 / 88.29%
Intronic: 5,868,829 / 8.52%
Intergenic: 2,193,991 / 3.19%
Intronic/intergenic overlapping exon: 2,414,822 / 3.51%

Transcript coverage profile

5' bias: 0.29
3' bias: 0.18
5'-3' bias: 1.9

Junction analysis

Reads at junctions: 20,162,559
ACCT 5.47%
AGGT 4.7%
ATCT 3.75%
AGGA 3.45%
TCCT 3.41%
GCCT 3.14%
AGCT 2.62%
CCCT 2.4%
AGGC 2.33%
TTCT 2.16%
AGAT 2.11%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis