Input data and parameters
Input
Analysis date: | Sun Oct 29 02:00:17 GMT 2023 |
BAM file: | SRX7354072.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): | 49,181,768 / 49,123,740 |
Number of aligned pairs (without duplicates): | 49,114,821 |
Total number of alignments: | 104,702,215 |
Number of secondary alignments: | 6,396,707 |
Number of non-unique alignments: | 10,367,089 |
Aligned to genes: | 81,391,955 |
Ambiguous alignments: | 295,939 |
No feature assigned: | 12,099,327 |
Missing chromosome in annotation: | 547,905 |
Not aligned: | 11,638,060 |
Reads genomic origin
Exonic: | 81,391,955 / 87.06% |
Intronic: | 7,611,904 / 8.14% |
Intergenic: | 4,487,423 / 4.8% |
Intronic/intergenic overlapping exon: | 3,387,779 / 3.62% |
Transcript coverage profile
5' bias: | 0.33 |
3' bias: | 0.21 |
5'-3' bias: | 1.81 |
Junction analysis
Reads at junctions: | 25,358,957 |
ACCT | 5.51% |
AGGT | 4.63% |
ATCT | 3.76% |
TCCT | 3.66% |
GCCT | 3.36% |
AGGA | 3.25% |
AGCT | 2.6% |
CCCT | 2.55% |
AGGC | 2.4% |
TTCT | 2.23% |
AGAT | 2.06% |