Input data and parameters
Input
Analysis date: | Tue Oct 31 09:39:09 GMT 2023 |
BAM file: | SRX7354313.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): | 46,129,012 / 46,097,352 |
Number of aligned pairs (without duplicates): | 46,081,646 |
Total number of alignments: | 102,923,380 |
Number of secondary alignments: | 10,697,016 |
Number of non-unique alignments: | 15,448,282 |
Aligned to genes: | 76,809,627 |
Ambiguous alignments: | 323,984 |
No feature assigned: | 8,582,873 |
Missing chromosome in annotation: | 1,758,614 |
Not aligned: | 6,293,870 |
Reads genomic origin
Exonic: | 76,809,627 / 89.95% |
Intronic: | 4,911,703 / 5.75% |
Intergenic: | 3,671,170 / 4.3% |
Intronic/intergenic overlapping exon: | 3,282,615 / 3.84% |
Transcript coverage profile
5' bias: | 0.05 |
3' bias: | 0.09 |
5'-3' bias: | 2.51 |
Junction analysis
Reads at junctions: | 19,910,452 |
TCCT | 6.7% |
CCCT | 6.21% |
ACCT | 4.84% |
ATCT | 4.83% |
AGGT | 3.58% |
AGGA | 2.81% |
GTCT | 2.51% |
TCCG | 2.11% |
TTCT | 1.96% |
AGGC | 1.93% |
GCCT | 1.88% |