Input data and parameters 

Input

Analysis date: Tue Oct 31 09:36:33 GMT 2023
BAM file: SRX7354344.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): 38,731,464 / 38,697,306
Number of aligned pairs (without duplicates): 38,693,744
Total number of alignments: 82,525,911
Number of secondary alignments: 5,097,141
Number of non-unique alignments: 8,680,446
Aligned to genes: 65,071,975
Ambiguous alignments: 240,079
No feature assigned: 8,244,553
Missing chromosome in annotation: 288,858
Not aligned: 3,129,702

Reads genomic origin

Exonic: 65,071,975 / 88.75%
Intronic: 5,229,003 / 7.13%
Intergenic: 3,015,550 / 4.11%
Intronic/intergenic overlapping exon: 2,409,472 / 3.29%

Transcript coverage profile

5' bias: 0.31
3' bias: 0.2
5'-3' bias: 1.85

Junction analysis

Reads at junctions: 19,444,197
ACCT 5.34%
AGGT 4.6%
ATCT 3.68%
TCCT 3.67%
AGGA 3.46%
GCCT 3.34%
AGCT 2.64%
CCCT 2.61%
AGGC 2.44%
AGAT 2.23%
TTCT 2.16%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis