Input data and parameters
Input
Analysis date: | Tue Oct 31 17:45:45 GMT 2023 |
BAM file: | SRX7354409.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): | 56,903,112 / 56,866,497 |
Number of aligned pairs (without duplicates): | 56,861,803 |
Total number of alignments: | 122,002,576 |
Number of secondary alignments: | 8,232,967 |
Number of non-unique alignments: | 12,661,324 |
Aligned to genes: | 88,121,710 |
Ambiguous alignments: | 345,631 |
No feature assigned: | 19,886,966 |
Missing chromosome in annotation: | 986,945 |
Not aligned: | 4,511,863 |
Reads genomic origin
Exonic: | 88,121,710 / 81.59% |
Intronic: | 13,946,910 / 12.91% |
Intergenic: | 5,940,056 / 5.5% |
Intronic/intergenic overlapping exon: | 3,942,835 / 3.65% |
Transcript coverage profile
5' bias: | 0.53 |
3' bias: | 0.33 |
5'-3' bias: | 1.65 |
Junction analysis
Reads at junctions: | 36,835,913 |
ACCT | 5.21% |
AGGT | 4.66% |
TCCT | 3.53% |
AGGA | 3.41% |
GCCT | 3.36% |
ATCT | 3.35% |
AGCT | 2.8% |
CCCT | 2.59% |
AGGC | 2.46% |
AGAT | 2.18% |
TTCT | 2.09% |