Input data and parameters
QualiMap command line
| qualimap bamqc -bam /kb/module/work/tmp/download_1de82232-ed37-4427-a15b-bfdf4b28d3d0/reads_alignment.bam -c -nw 400 -hm 3 |
Alignment
| Command line: | "/kb/module/bowtie2-bin/bowtie2-align-s --wrapper basic-0 -x SPAdes.Assembly -S /kb/module/work/tmp/bowtie2_alignment_output_16460837426607/reads_alignment.sam --phred33 --end-to-end --trim5 0 --trim3 0 --np 1 --minins 0 --maxins 500 -a -1 /kb/module/work/tmp/9f6c8beb-7feb-40b2-9c50-689eb3d988f7.fwd.fastq -2 /kb/module/work/tmp/5bdc79eb-402c-4702-8c48-dc2159fbd6fd.rev.fastq" |
| Draw chromosome limits: | yes |
| Analyze overlapping paired-end reads: | no |
| Program: | bowtie2 (2.3.2) |
| Analysis date: | Mon Feb 28 21:45:00 UTC 2022 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | no |
| Number of windows: | 400 |
| BAM file: | /kb/module/work/tmp/download_1de82232-ed37-4427-a15b-bfdf4b28d3d0/reads_alignment.bam |
Summary
Globals
| Reference size | 3,102,801 |
| Number of reads | 2,906,346 |
| Mapped reads | 2,895,545 / 99.63% |
| Unmapped reads | 10,801 / 0.37% |
| Mapped paired reads | 2,895,545 / 99.63% |
| Mapped reads, first in pair | 1,448,999 / 49.86% |
| Mapped reads, second in pair | 1,446,546 / 49.77% |
| Mapped reads, both in pair | 2,889,270 / 99.41% |
| Mapped reads, singletons | 6,275 / 0.22% |
| Secondary alignments | 7,697 |
| Read min/max/mean length | 36 / 151 / 145.45 |
| Duplicated reads (estimated) | 1,849,328 / 63.63% |
| Duplication rate | 58.09% |
| Clipped reads | 0 / 0% |
ACGT Content
| Number/percentage of A's | 110,578,645 / 26.32% |
| Number/percentage of C's | 98,457,671 / 23.44% |
| Number/percentage of T's | 112,066,658 / 26.68% |
| Number/percentage of G's | 98,866,302 / 23.53% |
| Number/percentage of N's | 124,651 / 0.03% |
| GC Percentage | 46.97% |
Coverage
| Mean | 135.4003 |
| Standard Deviation | 69.053 |
Mapping Quality
| Mean Mapping Quality | 254.73 |
Insert size
| Mean | 405.93 |
| Standard Deviation | 9,346.48 |
| P25/Median/P75 | 251 / 315 / 392 |
Mismatches and indels
| General error rate | 0.23% |
| Mismatches | 816,180 |
| Insertions | 18,747 |
| Mapped reads with at least one insertion | 0.57% |
| Deletions | 8,024 |
| Mapped reads with at least one deletion | 0.27% |
| Homopolymer indels | 41% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| NODE_1_length_2180415_cov_56.931963 | 2180415 | 261826984 | 120.0813 | 28.37 |
| NODE_2_length_325363_cov_77.098944 | 325363 | 53022655 | 162.9646 | 39.2198 |
| NODE_3_length_257272_cov_82.828340 | 257272 | 44942859 | 174.6901 | 26.1634 |
| NODE_4_length_223784_cov_68.824596 | 223784 | 32513155 | 145.2881 | 32.9126 |
| NODE_5_length_54497_cov_89.682268 | 54497 | 10268351 | 188.4205 | 27.1781 |
| NODE_6_length_41535_cov_83.179965 | 41535 | 7262397 | 174.8501 | 23.4242 |
| NODE_7_length_14203_cov_88.161192 | 14203 | 2598849 | 182.9789 | 32.3303 |
| NODE_8_length_3292_cov_686.091700 | 3292 | 5189528 | 1,576.4058 | 432.6763 |
| NODE_9_length_1507_cov_782.084615 | 1507 | 2326757 | 1,543.9662 | 336.2479 |
| NODE_10_length_933_cov_95.964953 | 933 | 168518 | 180.6195 | 49.8334 |
