Input data and parameters
Input
Analysis date: | Tue Oct 31 15:57:03 GMT 2023 |
BAM file: | SRX7354396.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): | 31,621,771 / 31,440,637 |
Number of aligned pairs (without duplicates): | 31,403,515 |
Total number of alignments: | 69,129,373 |
Number of secondary alignments: | 6,066,965 |
Number of non-unique alignments: | 9,293,554 |
Aligned to genes: | 44,775,556 |
Ambiguous alignments: | 195,737 |
No feature assigned: | 14,125,368 |
Missing chromosome in annotation: | 739,158 |
Not aligned: | 5,827,578 |
Reads genomic origin
Exonic: | 44,775,556 / 76.02% |
Intronic: | 6,671,767 / 11.33% |
Intergenic: | 7,453,601 / 12.65% |
Intronic/intergenic overlapping exon: | 2,616,658 / 4.44% |
Transcript coverage profile
5' bias: | 0.26 |
3' bias: | 0.22 |
5'-3' bias: | 1.76 |
Junction analysis
Reads at junctions: | 17,132,230 |
ACCT | 5.17% |
ATCT | 4.6% |
TCCT | 4.51% |
AGGT | 4.25% |
GCCT | 3.45% |
CCCT | 2.87% |
AGGA | 2.87% |
TTCT | 2.47% |
AGCT | 2.24% |
AGGC | 2.05% |
GTCT | 2.04% |