Input data and parameters 

Input

Analysis date: Tue Oct 31 09:16:57 GMT 2023
BAM file: SRX7354323.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): 36,019,904 / 35,981,957
Number of aligned pairs (without duplicates): 35,977,352
Total number of alignments: 77,028,351
Number of secondary alignments: 5,026,490
Number of non-unique alignments: 8,620,465
Aligned to genes: 58,961,636
Ambiguous alignments: 207,409
No feature assigned: 8,971,461
Missing chromosome in annotation: 267,380
Not aligned: 7,788,733

Reads genomic origin

Exonic: 58,961,636 / 86.79%
Intronic: 6,153,327 / 9.06%
Intergenic: 2,818,134 / 4.15%
Intronic/intergenic overlapping exon: 2,577,411 / 3.79%

Transcript coverage profile

5' bias: 0.38
3' bias: 0.2
5'-3' bias: 1.98

Junction analysis

Reads at junctions: 22,293,640
ACCT 5.55%
AGGT 4.68%
ATCT 3.65%
AGGA 3.47%
GCCT 3.36%
TCCT 3.34%
AGCT 2.66%
AGGC 2.38%
CCCT 2.37%
AGAT 2.25%
TTCT 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