Input data and parameters
Input
Analysis date: | Tue Oct 31 10:04:10 GMT 2023 |
BAM file: | SRX7354331.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): | 57,922,780 / 57,795,728 |
Number of aligned pairs (without duplicates): | 57,781,796 |
Total number of alignments: | 122,855,076 |
Number of secondary alignments: | 7,136,568 |
Number of non-unique alignments: | 11,349,271 |
Aligned to genes: | 92,481,700 |
Ambiguous alignments: | 356,800 |
No feature assigned: | 17,946,866 |
Missing chromosome in annotation: | 720,439 |
Not aligned: | 27,840,528 |
Reads genomic origin
Exonic: | 92,481,700 / 83.75% |
Intronic: | 12,154,731 / 11.01% |
Intergenic: | 5,792,135 / 5.25% |
Intronic/intergenic overlapping exon: | 4,570,860 / 4.14% |
Transcript coverage profile
5' bias: | 0.45 |
3' bias: | 0.3 |
5'-3' bias: | 1.65 |
Junction analysis
Reads at junctions: | 39,181,914 |
ACCT | 5.15% |
AGGT | 4.73% |
TCCT | 3.7% |
ATCT | 3.52% |
AGGA | 3.37% |
GCCT | 3.28% |
AGCT | 2.77% |
CCCT | 2.75% |
AGGC | 2.51% |
AGAT | 2.04% |
TTCT | 2.04% |