Dante Labs (WGS)

[JamesKane]

Before filtering
total reads: 667.495810 M
total bases: 99.125328 G
Q20 bases: 96.030385 G (96.877748%)
Q30 bases: 90.925155 G (91.727470%)
GC content: 43.566229%
After filtering
total reads: 662.534472 M
total bases: 98.299320 G
Q20 bases: 95.480444 G (97.132355%)
Q30 bases: 90.481013 G (92.046428%)
GC content: 43.541445%
Filtering result

A 30x WGS test should have better than 90gBases. These files easily exceed that amount.

Now the BAM should be investigated for genomic territory covered. You could use GATK's CollectWgsMetrics. MEAN_COVERAGE should be about 30x. If it's significantly lower, you had a higher bacterial concentration sequenced than normal.

[JamesKane]

Before filtering
total reads: 834.317408 M
total bases: 125.147611 G
Q20 bases: 121.528261 G (97.107935%)
Q30 bases: 115.666626 G (92.424158%)
GC content: 40.918799%
After filtering
total reads: 827.816768 M
total bases: 123.827389 G
Q20 bases: 120.561766 G (97.362762%)
Q30 bases: 114.859232 G (92.757534%)
GC content: 40.873596%

Much higher than expected. That's closer to 40x coverage and would be atypical.

[JamesKane]

Before filtering
total reads: 347.074070 M
total bases: 51.605934 G
Q20 bases: 49.989405 G (96.867553%)
Q30 bases: 47.543664 G (92.128290%)
GC content: 42.797089%
After filtering
total reads: 342.757768 M
total bases: 50.954371 G
Q20 bases: 49.556123 G (97.255882%)
Q30 bases: 47.189698 G (92.611679%)
GC content: 42.717622%

Helps to confirm what I've seen in the Y-chromosome data added to the Y-DNA Warehouse. These tests are actually 15x+ to date. The real question is why are they overshooting the mark so much? Why not market as 15x if this is expected?

[Petr]

Summary of all my WGS 30x tests from Dante, total bases after filtering and coverage calculated for idxstats:

2018-01-19: 118 G - 32.8x - 12.4 % of unmapped reads
2018-03-23: 125 G - 32.7x - 8.3 % of unmapped reads
2019-03-27: 124 G - 38.7x - 1.8 % of unmapped reads
2019-03-27: 89 G - 27.5x - 3.3 % of unmapped reads
2019-03-27: 102 G - 25.5x - 20.7 % of unmapped reads
2019-03-27: 93 G - 21.0x - 28.5 % of unmapped reads
2019-06-05: 106 G - 29.4x - 12.8 % of unmapped reads
2019-11-12: 98 G - mapping not processed yet
2019-11-14: 73.7 G - mapping not processed yet

[teepean47]

Helps to confirm what I've seen in the Y-chromosome data added to the Y-DNA Warehouse. These tests are actually 15x+ to date. The real question is why are they overshooting the mark so much? Why not market as 15x if this is expected?

Weird thing is that YFull refused to accept this. According to their customer service: "Unfortunately, the quality of the sequence is extremely low for the Y chromosome".

[MacUalraig]

Weird thing is that YFull refused to accept this. According to their customer service: "Unfortunately, the quality of the sequence is extremely low for the Y chromosome".

Can you ask them for the stats they used to reject it? If its not a trade secret.

[teepean47]

Can you ask them for the stats they used to reject it? If its not a trade secret.

The only answer I got was it is 2x. I did ask again but I doubt I get an answer. Maybe they don't want to anger their new business partner... I honestly thought Dante's 4X would be the perfect cheap test to cover everything.

[Petr]

The results of WGS 30x received today have somewhat lower average number of reads:

General
fastp version: 0.20.0 (https://github.com/OpenGene/fastp)
sequencing: paired end (151 cycles + 151 cycles)
mean length before filtering: 148bp, 148bp
mean length after filtering: 148bp, 148bp
duplication rate: 5.775481%
Insert size peak: 261
Before filtering
total reads: 502.517378 M
total bases: 74.698229 G
Q20 bases: 72.112478 G (96.538403%)
Q30 bases: 68.185465 G (91.281233%)
GC content: 41.676315%
After filtering
total reads: 497.104320 M
total bases: 73.690341 G
Q20 bases: 71.416587 G (96.914448%)
Q30 bases: 67.614213 G (91.754512%)
GC content: 41.600758%
Filtering result
reads passed filters: 497.104320 M (98.922812%)
reads with low quality: 5.140478 M (1.022945%)
reads with too many N: 31.094000 K (0.006188%)
reads too short: 241.486000 K (0.048055%)

[mdn]

The only answer I got was it is 2x. I did ask again but I doubt I get an answer. Maybe they don't want to anger their new business partner... I honestly thought Dante's 4X would be the perfect cheap test to cover everything.

Please could you clarify is your results filtered for Y only or not?

For example here https://anthrogenica.com/showthread....l=1#post611568 statistics for 4x says: "ChrY... 29.20% Coverage and 1.66 Mean Depth" Could you show your output by BamDeal?

As Y DNA Warehouse statistics page also says: "On average WGS tests have fifty percent of test's rated depth covered in the Y chromosome e.g. a 15x test has 7 reads spanning each location". 4x -> 2x should be ok.

I am considering 4x as a great (and very cheap) option to get a brief autosomal DNA + mtDNA + might be some of Y (if it is possible), so it would be nice even if sometime accidentally they are producing better Y results.

[MacUalraig]

For comparison I once loaded a WGSx4 (FGC low pass) to YFull and have several YSEQ with a Y depth median 7-8x, my worst YSEQ has been 6x (on the Y) and those were all accepted. YFull have a very good relationship with YSEQ of course.

I didn't bother uploading my WGSx2 though.