Input data and parameters 

Input

Analysis date: Mon Oct 30 20:24:09 GMT 2023
BAM file: SRX7354233.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): 35,441,710 / 35,420,204
Number of aligned pairs (without duplicates): 35,417,097
Total number of alignments: 74,624,108
Number of secondary alignments: 3,762,194
Number of non-unique alignments: 6,244,653
Aligned to genes: 58,085,125
Ambiguous alignments: 185,103
No feature assigned: 9,843,018
Missing chromosome in annotation: 266,209
Not aligned: 2,047,928

Reads genomic origin

Exonic: 58,085,125 / 85.51%
Intronic: 7,152,969 / 10.53%
Intergenic: 2,690,049 / 3.96%
Intronic/intergenic overlapping exon: 2,376,602 / 3.5%

Transcript coverage profile

5' bias: 0.43
3' bias: 0.13
5'-3' bias: 2.49

Junction analysis

Reads at junctions: 18,484,905
ACCT 5.5%
AGGT 4.73%
ATCT 3.62%
AGGA 3.6%
TCCT 3.54%
GCCT 3.05%
AGCT 2.68%
AGGC 2.39%
AGAT 2.3%
CCCT 2.22%
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