Input data and parameters
Input
Analysis date: | Tue Oct 31 09:22:14 GMT 2023 |
BAM file: | SRX7354317.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): | 54,016,946 / 53,903,667 |
Number of aligned pairs (without duplicates): | 53,876,686 |
Total number of alignments: | 114,719,360 |
Number of secondary alignments: | 6,798,747 |
Number of non-unique alignments: | 11,461,059 |
Aligned to genes: | 90,728,969 |
Ambiguous alignments: | 315,339 |
No feature assigned: | 11,894,619 |
Missing chromosome in annotation: | 319,374 |
Not aligned: | 11,310,349 |
Reads genomic origin
Exonic: | 90,728,969 / 88.41% |
Intronic: | 8,004,695 / 7.8% |
Intergenic: | 3,889,924 / 3.79% |
Intronic/intergenic overlapping exon: | 4,053,374 / 3.95% |
Transcript coverage profile
5' bias: | 0.24 |
3' bias: | 0.15 |
5'-3' bias: | 1.78 |
Junction analysis
Reads at junctions: | 28,960,168 |
ACCT | 5.58% |
AGGT | 4.54% |
ATCT | 3.88% |
TCCT | 3.54% |
GCCT | 3.44% |
AGGA | 3.28% |
AGCT | 2.48% |
CCCT | 2.42% |
AGGC | 2.28% |
TTCT | 2.21% |
AGAT | 2.01% |