Input data and parameters
Input
Analysis date: | Tue Oct 31 08:56:48 GMT 2023 |
BAM file: | SRX7354294.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): | 34,593,274 / 34,576,478 |
Number of aligned pairs (without duplicates): | 34,573,819 |
Total number of alignments: | 73,369,404 |
Number of secondary alignments: | 4,199,652 |
Number of non-unique alignments: | 6,892,288 |
Aligned to genes: | 57,625,501 |
Ambiguous alignments: | 223,138 |
No feature assigned: | 8,323,379 |
Missing chromosome in annotation: | 305,098 |
Not aligned: | 1,433,794 |
Reads genomic origin
Exonic: | 57,625,501 / 87.38% |
Intronic: | 6,115,455 / 9.27% |
Intergenic: | 2,207,924 / 3.35% |
Intronic/intergenic overlapping exon: | 2,190,900 / 3.32% |
Transcript coverage profile
5' bias: | 0.33 |
3' bias: | 0.18 |
5'-3' bias: | 1.96 |
Junction analysis
Reads at junctions: | 19,560,796 |
ACCT | 5.49% |
AGGT | 4.65% |
ATCT | 3.57% |
AGGA | 3.56% |
TCCT | 3.35% |
GCCT | 3.34% |
AGCT | 2.74% |
CCCT | 2.41% |
AGGC | 2.4% |
AGAT | 2.28% |
TTCT | 2.17% |