Input data and parameters
Input
Analysis date: | Tue Oct 31 09:52:26 GMT 2023 |
BAM file: | SRX7354361.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): | 26,929,969 / 26,913,475 |
Number of aligned pairs (without duplicates): | 26,911,681 |
Total number of alignments: | 57,201,849 |
Number of secondary alignments: | 3,358,405 |
Number of non-unique alignments: | 5,703,861 |
Aligned to genes: | 44,822,964 |
Ambiguous alignments: | 155,899 |
No feature assigned: | 6,341,256 |
Missing chromosome in annotation: | 177,869 |
Not aligned: | 1,221,126 |
Reads genomic origin
Exonic: | 44,822,964 / 87.61% |
Intronic: | 4,420,807 / 8.64% |
Intergenic: | 1,920,449 / 3.75% |
Intronic/intergenic overlapping exon: | 1,713,221 / 3.35% |
Transcript coverage profile
5' bias: | 0.39 |
3' bias: | 0.22 |
5'-3' bias: | 1.85 |
Junction analysis
Reads at junctions: | 14,353,434 |
ACCT | 5.27% |
AGGT | 4.6% |
ATCT | 3.74% |
TCCT | 3.54% |
AGGA | 3.53% |
GCCT | 3.23% |
AGCT | 2.71% |
CCCT | 2.47% |
AGGC | 2.36% |
AGAT | 2.24% |
TTCT | 2.09% |