Input data and parameters 

Input

Analysis date: Tue Oct 31 10:01:17 GMT 2023
BAM file: SRX7354381.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): 29,014,694 / 28,986,770
Number of aligned pairs (without duplicates): 28,982,148
Total number of alignments: 62,474,425
Number of secondary alignments: 4,472,961
Number of non-unique alignments: 6,864,462
Aligned to genes: 48,071,927
Ambiguous alignments: 180,159
No feature assigned: 6,788,576
Missing chromosome in annotation: 569,301
Not aligned: 3,511,822

Reads genomic origin

Exonic: 48,071,927 / 87.63%
Intronic: 4,836,409 / 8.82%
Intergenic: 1,952,167 / 3.56%
Intronic/intergenic overlapping exon: 1,859,761 / 3.39%

Transcript coverage profile

5' bias: 0.34
3' bias: 0.19
5'-3' bias: 2

Junction analysis

Reads at junctions: 16,035,036
ACCT 5.52%
AGGT 4.65%
ATCT 3.59%
AGGA 3.49%
TCCT 3.44%
GCCT 3.24%
AGCT 2.74%
CCCT 2.43%
AGGC 2.37%
AGAT 2.19%
TTCT 2.13%

Reads Genomic Origin 

Coverage Profile Along Genes (Total) 

Coverage Profile Along Genes (Low) 

Coverage Profile Along Genes (High) 

Coverage Histogram (0-50X) 

Junction Analysis