Input data and parameters
QualiMap command line
| qualimap bamqc -bam /data/dnb03/galaxy_db/files/f/1/3/dataset_f13c4a84-bf51-46a7-ae2c-1e3d6ae38a00.dat -c -nw 400 -hm 3 -sd |
Alignment
| Command line: | bwa mem -t 8 -v 1 -R @RG\tID:Cutadapt_on_data_12_and_data_11__Read_\tSM:Cutadapt_on_data_12_and_data_11__Read_\tPL:ILLUMINA\tLB:Cutadapt_on_data_12_and_data_11__Read_\tPU:run /data/db/data_managers/hg19/bwa_mem_index/hg19/hg19.fa /data/dnb03/galaxy_db/files/4/3/8/dataset_4385aff9-5bb6-480d-a31a-4a47956619aa.dat /data/dnb03/galaxy_db/files/4/3/c/dataset_43c7ecfd-43ee-4c52-8b82-3fd62b5faf27.dat |
| Draw chromosome limits: | yes |
| Analyze overlapping paired-end reads: | yes |
| Program: | bwa (0.7.17-r1188) |
| Analysis date: | Sat May 22 06:50:50 CEST 2021 |
| Size of a homopolymer: | 3 |
| Skip duplicate alignments: | yes (only flagged) |
| Number of windows: | 400 |
| BAM file: | /data/dnb03/galaxy_db/files/f/1/3/dataset_f13c4a84-bf51-46a7-ae2c-1e3d6ae38a00.dat |
Summary
Warnings
| No flagged duplicates are detected | Make sure duplicate alignments are flagged in the BAM file or apply a different skip duplicates mode. |
Globals
| Reference size | 3,137,161,264 |
| Number of reads | 66,254,428 |
| Mapped reads | 66,164,253 / 99.86% |
| Unmapped reads | 90,175 / 0.14% |
| Mapped paired reads | 66,164,253 / 99.86% |
| Mapped reads, first in pair | 33,091,227 / 49.95% |
| Mapped reads, second in pair | 33,073,026 / 49.92% |
| Mapped reads, both in pair | 66,138,992 / 99.83% |
| Mapped reads, singletons | 25,261 / 0.04% |
| Secondary alignments | 0 |
| Supplementary alignments | 161,322 / 0.24% |
| Read min/max/mean length | 20 / 101 / 99.62 |
| Overlapping read pairs | 5,152,376 / 15.55% |
| Duplicated reads (flagged) | 0 / 0% |
| Duplicated reads (estimated) | 26,326,731 / 39.74% |
| Duplication rate | 31.53% |
| Clipped reads | 983,259 / 1.48% |
ACGT Content
| Number/percentage of A's | 1,548,019,101 / 23.54% |
| Number/percentage of C's | 1,748,497,866 / 26.59% |
| Number/percentage of T's | 1,562,639,202 / 23.76% |
| Number/percentage of G's | 1,716,770,090 / 26.11% |
| Number/percentage of N's | 138,944 / 0% |
| GC Percentage | 52.7% |
Coverage
| Mean | 2.0964 |
| Standard Deviation | 27.1606 |
| Mean (paired-end reads overlap ignored) | 2.05 |
Mapping Quality
| Mean Mapping Quality | 46.49 |
Insert size
| Mean | 70,424.26 |
| Standard Deviation | 2,625,027.22 |
| P25/Median/P75 | 219 / 263 / 316 |
Mismatches and indels
| General error rate | 0.23% |
| Mismatches | 14,480,525 |
| Insertions | 234,116 |
| Mapped reads with at least one insertion | 0.35% |
| Deletions | 309,457 |
| Mapped reads with at least one deletion | 0.46% |
| Homopolymer indels | 44.59% |
Chromosome stats
| Name | Length | Mapped bases | Mean coverage | Standard deviation |
| chr10 | 135534747 | 242299294 | 1.7877 | 13.827 |
| chr11 | 135006516 | 341567309 | 2.53 | 16.2016 |
| chr11_gl000202_random | 40103 | 7210 | 0.1798 | 0.5064 |
| chr12 | 133851895 | 285765785 | 2.1349 | 13.4314 |
| chr13 | 115169878 | 98571143 | 0.8559 | 7.9165 |
| chr14 | 107349540 | 173138626 | 1.6128 | 13.8565 |
| chr15 | 102531392 | 284760755 | 2.7773 | 19.6507 |
| chr16 | 90354753 | 320513103 | 3.5473 | 21.9705 |
| chr17_ctg5_hap1 | 1680828 | 3070023 | 1.8265 | 9.6379 |
| chr17 | 81195210 | 404423155 | 4.9809 | 26.0257 |
| chr17_gl000203_random | 37498 | 2263 | 0.0603 | 0.2429 |
| chr17_gl000204_random | 81310 | 27171 | 0.3342 | 2.6608 |
| chr17_gl000205_random | 174588 | 961591 | 5.5078 | 47.1724 |
| chr17_gl000206_random | 41001 | 9528 | 0.2324 | 0.6593 |
| chr18 | 78077248 | 87485913 | 1.1205 | 12.7231 |
| chr18_gl000207_random | 4262 | 1415 | 0.332 | 0.666 |
| chr19 | 59128983 | 398390783 | 6.7377 | 27.5455 |
| chr19_gl000208_random | 92689 | 34337 | 0.3705 | 1.4499 |
| chr19_gl000209_random | 159169 | 359106 | 2.2561 | 10.5071 |
| chr1 | 249250621 | 664488991 | 2.6659 | 20.7099 |
| chr1_gl000191_random | 106433 | 168264 | 1.5809 | 6.286 |
| chr1_gl000192_random | 547496 | 1188328 | 2.1705 | 8.9335 |
| chr20 | 63025520 | 151192965 | 2.3989 | 15.7836 |
| chr21 | 48129895 | 74805426 | 1.5542 | 17.2004 |
| chr21_gl000210_random | 27682 | 5054 | 0.1826 | 0.7169 |
| chr22 | 51304566 | 194300248 | 3.7872 | 27.1111 |
| chr2 | 243199373 | 390593364 | 1.6061 | 12.9254 |
| chr3 | 198022430 | 324569556 | 1.6391 | 16.8528 |
| chr4_ctg9_hap1 | 590426 | 548606 | 0.9292 | 5.9314 |
| chr4 | 191154276 | 238326889 | 1.2468 | 22.0377 |
| chr4_gl000193_random | 189789 | 320088 | 1.6865 | 21.7917 |
| chr4_gl000194_random | 191469 | 1343844 | 7.0186 | 54.562 |
| chr5 | 180915260 | 297121505 | 1.6423 | 20.5682 |
| chr6_apd_hap1 | 4622290 | 3011522 | 0.6515 | 5.9657 |
| chr6_cox_hap2 | 4795371 | 7017079 | 1.4633 | 6.8809 |
| chr6_dbb_hap3 | 4610396 | 7767438 | 1.6848 | 7.9557 |
| chr6 | 171115067 | 233980804 | 1.3674 | 10.6851 |
| chr6_mann_hap4 | 4683263 | 5064456 | 1.0814 | 5.201 |
| chr6_mcf_hap5 | 4833398 | 7041753 | 1.4569 | 6.537 |
| chr6_qbl_hap6 | 4611984 | 6219698 | 1.3486 | 7.2018 |
| chr6_ssto_hap7 | 4928567 | 5695176 | 1.1555 | 5.7154 |
| chr7 | 159138663 | 445312508 | 2.7983 | 65.6965 |
| chr7_gl000195_random | 182896 | 983023 | 5.3748 | 46.4472 |
| chr8 | 146364022 | 380610434 | 2.6004 | 73.0434 |
| chr8_gl000196_random | 38914 | 19144 | 0.492 | 2.2742 |
| chr8_gl000197_random | 37175 | 44594 | 1.1996 | 5.6839 |
| chr9 | 141213431 | 288179022 | 2.0407 | 16.3728 |
| chr9_gl000198_random | 90085 | 92209 | 1.0236 | 8.8943 |
| chr9_gl000199_random | 169874 | 409276 | 2.4093 | 9.8227 |
| chr9_gl000200_random | 187035 | 113746 | 0.6082 | 4.5897 |
| chr9_gl000201_random | 36148 | 142801 | 3.9505 | 9.7414 |
| chrM | 16571 | 132215 | 7.9787 | 3.3079 |
| chrUn_gl000211 | 166566 | 1389196 | 8.3402 | 24.5069 |
| chrUn_gl000212 | 186858 | 4809803 | 25.7404 | 95.8274 |
| chrUn_gl000213 | 164239 | 814753 | 4.9608 | 40.8727 |
| chrUn_gl000214 | 137718 | 2273786 | 16.5104 | 49.2104 |
| chrUn_gl000215 | 172545 | 370919 | 2.1497 | 10.9309 |
| chrUn_gl000216 | 172294 | 277517 | 1.6107 | 9.4114 |
| chrUn_gl000217 | 172149 | 213237 | 1.2387 | 10.7992 |
| chrUn_gl000218 | 161147 | 1194655 | 7.4134 | 45.0032 |
| chrUn_gl000219 | 179198 | 509442 | 2.8429 | 28.6635 |
| chrUn_gl000220 | 161802 | 5689913 | 35.1659 | 242.0505 |
| chrUn_gl000221 | 155397 | 1797067 | 11.5644 | 44.1476 |
| chrUn_gl000222 | 186861 | 1024701 | 5.4838 | 34.9603 |
| chrUn_gl000223 | 180455 | 344938 | 1.9115 | 6.6837 |
| chrUn_gl000224 | 179693 | 170956 | 0.9514 | 3.1554 |
| chrUn_gl000225 | 211173 | 916807 | 4.3415 | 35.5378 |
| chrUn_gl000226 | 15008 | 289590 | 19.2957 | 14.431 |
| chrUn_gl000227 | 128374 | 724697 | 5.6452 | 35.1327 |
| chrUn_gl000228 | 129120 | 970622 | 7.5172 | 25.007 |
| chrUn_gl000229 | 19913 | 378281 | 18.9967 | 47.4149 |
| chrUn_gl000230 | 43691 | 123236 | 2.8206 | 9.9624 |
| chrUn_gl000231 | 27386 | 223064 | 8.1452 | 30.708 |
| chrUn_gl000232 | 40652 | 69463 | 1.7087 | 11.9834 |
| chrUn_gl000233 | 45941 | 3562 | 0.0775 | 0.2852 |
| chrUn_gl000234 | 40531 | 93363 | 2.3035 | 17.0263 |
| chrUn_gl000235 | 34474 | 79980 | 2.32 | 18.338 |
| chrUn_gl000236 | 41934 | 107671 | 2.5676 | 9.7259 |
| chrUn_gl000237 | 45867 | 149381 | 3.2568 | 19.5309 |
| chrUn_gl000238 | 39939 | 171656 | 4.298 | 14.5962 |
| chrUn_gl000239 | 33824 | 56746 | 1.6777 | 6.7089 |
| chrUn_gl000240 | 41933 | 53969 | 1.287 | 6.6748 |
| chrUn_gl000241 | 42152 | 167118 | 3.9647 | 15.2897 |
| chrUn_gl000242 | 43523 | 236937 | 5.4439 | 17.0542 |
| chrUn_gl000243 | 43341 | 52044 | 1.2008 | 6.6497 |
| chrUn_gl000244 | 39929 | 234753 | 5.8793 | 35.512 |
| chrUn_gl000245 | 36651 | 5237 | 0.1429 | 0.4043 |
| chrUn_gl000246 | 38154 | 23572 | 0.6178 | 3.66 |
| chrUn_gl000247 | 36422 | 7925 | 0.2176 | 1.0338 |
| chrUn_gl000248 | 39786 | 3403 | 0.0855 | 0.3028 |
| chrUn_gl000249 | 38502 | 39135 | 1.0164 | 4.0608 |
| chrX | 155270560 | 133354136 | 0.8589 | 7.0962 |
| chrY | 59373566 | 45197956 | 0.7612 | 13.4166 |
