Input data and parameters
QualiMap command line
| qualimap bamqc -bam DGY3_sorted_dedup.bam -nw 400 -hm 3 |
Alignment
| Command line: | bwa mem -K 100000000 -v 3 -t 10 -Y -R @RG\tID:DGY3\tLB:DGY3\tPL:illumina\tPM:nextseq\tSM:DGY3 /scratch/work/cgsb/genomes/Public/Fungi/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa DGY3_trimmed_1.fq.gz DGY3_trimmed_2.fq.gz |
| Draw chromosome limits: | no |
| Analyze overlapping paired-end reads: | no |
| Program: | bwa (0.7.17-r1188) |
| Analysis date: | Mon Oct 14 22:10:09 EDT 2024 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | DGY3_sorted_dedup.bam |
Summary
Globals
| Reference size | 12,157,105 |
| Number of reads | 5,399,790 |
| Mapped reads | 4,942,312 / 91.53% |
| Supplementary alignments | 2,680 / 0.05% |
| Unmapped reads | 457,478 / 8.47% |
| Mapped paired reads | 4,942,312 / 91.53% |
| Mapped reads, first in pair | 2,471,156 / 45.76% |
| Mapped reads, second in pair | 2,471,156 / 45.76% |
| Mapped reads, both in pair | 4,942,312 / 91.53% |
| Mapped reads, singletons | 0 / 0% |
| Read min/max/mean length | 20 / 151 / 117.18 |
| Duplicated reads (flagged) | 1,625,478 / 30.1% |
| Clipped reads | 385,228 / 7.13% |
ACGT Content
| Number/percentage of A's | 173,364,995 / 29.88% |
| Number/percentage of C's | 121,387,100 / 20.92% |
| Number/percentage of T's | 173,038,568 / 29.83% |
| Number/percentage of G's | 112,349,575 / 19.37% |
| Number/percentage of N's | 2,200 / 0% |
| GC Percentage | 40.29% |
Coverage
| Mean | 47.723 |
| Standard Deviation | 207.4807 |
Mapping Quality
| Mean Mapping Quality | 54.16 |
Insert size
| Mean | 25,331.77 |
| Standard Deviation | 97,875.48 |
| P25/Median/P75 | 9,138 / 9,138 / 9,138 |
Mismatches and indels
| General error rate | 0.06% |
| Mismatches | 327,997 |
| Insertions | 10,477 |
| Mapped reads with at least one insertion | 0.21% |
| Deletions | 23,529 |
| Mapped reads with at least one deletion | 0.47% |
| Homopolymer indels | 71.64% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| I | 230218 | 11570780 | 50.2601 | 31.9824 |
| II | 813184 | 31743724 | 39.0363 | 29.775 |
| III | 316620 | 15389827 | 48.6066 | 34.7832 |
| IV | 1531933 | 55220599 | 36.0464 | 27.6878 |
| V | 576874 | 24899253 | 43.1624 | 28.8222 |
| VI | 270161 | 11748273 | 43.4862 | 35.1308 |
| VII | 1090940 | 42469418 | 38.9292 | 29.8027 |
| VIII | 562643 | 20003590 | 35.5529 | 28.3646 |
| IX | 439888 | 18573355 | 42.2229 | 28.346 |
| X | 745751 | 27644091 | 37.0688 | 27.0341 |
| XI | 666816 | 22762191 | 34.1356 | 27.9046 |
| XII | 1078177 | 135846723 | 125.9967 | 680.3868 |
| XIII | 924431 | 38331480 | 41.4649 | 28.7332 |
| XIV | 784333 | 31289065 | 39.8926 | 27.969 |
| XV | 1091291 | 42976000 | 39.3809 | 29.2246 |
| XVI | 948066 | 37777027 | 39.8464 | 30.0353 |
| Mito | 85779 | 11928570 | 139.0617 | 279.0326 |
