Input data and parameters
Input
Analysis date: | Mon Oct 30 22:59:33 GMT 2023 |
BAM file: | SRX7354228.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): | 44,902,147 / 44,860,642 |
Number of aligned pairs (without duplicates): | 44,840,145 |
Total number of alignments: | 95,210,306 |
Number of secondary alignments: | 5,447,517 |
Number of non-unique alignments: | 8,989,643 |
Aligned to genes: | 75,360,413 |
Ambiguous alignments: | 257,877 |
No feature assigned: | 10,170,501 |
Missing chromosome in annotation: | 431,872 |
Not aligned: | 690,225 |
Reads genomic origin
Exonic: | 75,360,413 / 88.11% |
Intronic: | 6,511,971 / 7.61% |
Intergenic: | 3,658,530 / 4.28% |
Intronic/intergenic overlapping exon: | 3,640,492 / 4.26% |
Transcript coverage profile
5' bias: | 0.39 |
3' bias: | 0.23 |
5'-3' bias: | 1.87 |
Junction analysis
Reads at junctions: | 23,212,085 |
ACCT | 5.43% |
AGGT | 4.63% |
TCCT | 3.55% |
ATCT | 3.45% |
GCCT | 3.38% |
AGGA | 3.32% |
AGCT | 2.72% |
CCCT | 2.53% |
AGGC | 2.4% |
TTCT | 2.05% |
AGAT | 2% |