Input data and parameters 

Input

Analysis date: Tue Oct 31 09:46:08 GMT 2023
BAM file: SRX7354262.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): 77,335,447 / 77,293,051
Number of aligned pairs (without duplicates): 77,286,095
Total number of alignments: 166,269,135
Number of secondary alignments: 11,640,637
Number of non-unique alignments: 16,825,632
Aligned to genes: 127,306,360
Ambiguous alignments: 625,296
No feature assigned: 19,475,202
Missing chromosome in annotation: 2,036,645
Not aligned: 3,611,796

Reads genomic origin

Exonic: 127,306,360 / 86.73%
Intronic: 11,572,423 / 7.88%
Intergenic: 7,902,779 / 5.38%
Intronic/intergenic overlapping exon: 6,355,357 / 4.33%

Transcript coverage profile

5' bias: 0.29
3' bias: 0.27
5'-3' bias: 1.76

Junction analysis

Reads at junctions: 53,989,479
ACCT 5.22%
TCCT 4.66%
AGGT 4.51%
ATCT 4.1%
GCCT 3.65%
CCCT 2.95%
AGGA 2.91%
AGGC 2.45%
AGCT 2.37%
TTCT 2.29%
GTCT 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