Input data and parameters
Input
Analysis date: | Sun Oct 29 03:11:15 GMT 2023 |
BAM file: | SRX7354128.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): | 46,032,500 / 45,962,552 |
Number of aligned pairs (without duplicates): | 45,956,236 |
Total number of alignments: | 97,964,144 |
Number of secondary alignments: | 5,969,092 |
Number of non-unique alignments: | 10,173,868 |
Aligned to genes: | 76,203,919 |
Ambiguous alignments: | 243,861 |
No feature assigned: | 11,005,406 |
Missing chromosome in annotation: | 337,090 |
Not aligned: | 6,763,126 |
Reads genomic origin
Exonic: | 76,203,919 / 87.38% |
Intronic: | 6,821,866 / 7.82% |
Intergenic: | 4,183,540 / 4.8% |
Intronic/intergenic overlapping exon: | 2,978,549 / 3.42% |
Transcript coverage profile
5' bias: | 0.28 |
3' bias: | 0.18 |
5'-3' bias: | 1.76 |
Junction analysis
Reads at junctions: | 22,900,508 |
ACCT | 5.45% |
AGGT | 4.57% |
ATCT | 3.59% |
AGGA | 3.53% |
TCCT | 3.3% |
GCCT | 3.28% |
AGCT | 2.72% |
CCCT | 2.38% |
AGGC | 2.34% |
AGAT | 2.27% |
TTCT | 2.22% |