Input data and parameters
Input
Analysis date: | Tue Oct 31 09:35:33 GMT 2023 |
BAM file: | SRX7354340.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): | 38,571,961 / 38,542,026 |
Number of aligned pairs (without duplicates): | 38,538,312 |
Total number of alignments: | 82,483,363 |
Number of secondary alignments: | 5,369,376 |
Number of non-unique alignments: | 8,869,599 |
Aligned to genes: | 66,456,211 |
Ambiguous alignments: | 269,011 |
No feature assigned: | 6,484,329 |
Missing chromosome in annotation: | 404,213 |
Not aligned: | 5,625,105 |
Reads genomic origin
Exonic: | 66,456,211 / 91.11% |
Intronic: | 3,723,038 / 5.1% |
Intergenic: | 2,761,291 / 3.79% |
Intronic/intergenic overlapping exon: | 2,405,398 / 3.3% |
Transcript coverage profile
5' bias: | 0.23 |
3' bias: | 0.21 |
5'-3' bias: | 1.64 |
Junction analysis
Reads at junctions: | 20,684,999 |
ACCT | 5.43% |
AGGT | 4.5% |
ATCT | 4.46% |
TCCT | 4.1% |
GCCT | 3.57% |
CCCT | 3.01% |
AGGA | 3.01% |
AGCT | 2.36% |
TTCT | 2.36% |
AGGC | 2.26% |
AGAA | 1.78% |