Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications

Table 1 Estimating θ with constant sequencing error rate

Error rate	Sites used	θ = 0.1 / kb			θ = 1 / kb
Error rate	Sites used	Single line	Pooled-lines		Single line	Pooled-lines
			single platform	dual applications		single platform	dual applications
	S_>0	0.099 (0.007)	0.100 (0.003)	0.100 (0.007)	0.999 (0.023)	1.000 (0.009)	0.999 (0.022)
0	S_>1	0.100 (0.012)	0.100 (0.005)	0.100 (0.010)	0.999 (0.041)	1.000 (0.016)	1.000 (0.034)
	S_>2	0.099 (0.016)	0.100 (0.007)	0.100 (0.013)	0.998 (0.050)	1.000 (0.023)	1.000 (0.041)
	S_>0	5.992 (0.131)	22.054 (0.212)	0.323 (0.026)	6.884 (0.131)	22.872 (0.225)	1.226 (0.033)
0.001	S_>1	0.129 (0.017)	0.507 (0.032)	0.100 (0.011)	1.032 (0.040)	1.409 (0.035)	1.003 (0.034)
	S_>2	0.101 (0.017)	0.105 (0.008)	0.100 (0.013)	0.999 (0.052)	1.009 (0.023)	1.002 (0.042)
	S_>0	28.389 (0.271)	90.901 (0.357)	5.269 (0.116)	29.184 (0.275)	91.485 (0.358)	6.165 (0.118)
0.005	S_>1	0.810 (0.054)	9.295 (0.149)	0.112 (0.012)	1.716 (0.064)	10.167 (0.152)	1.024 (0.035)
	S_>2	0.112 (0.017)	0.662 (0.039)	0.100 (0.014)	1.016 (0.053)	1.575 (0.046)	1.010 (0.042)
	S_>0	53.883 (0.351)	146.007 (0.357)	18.820 (0.215)	54.615 (0.331)	146.329 (1.111)	19.684 (0.218)
0.01	S_>1	2.861 (0.105)	31.994 (0.258)	0.257 (0.025)	3.777 (0.107)	32.823 (0.821)	1.179 (0.040)
	S_>2	0.180 (0.027)	4.061 (0.108)	0.102 (0.013)	1.091 (0.057)	4.993 (0.327)	1.017 (0.041)

The average depth is 2X per individual in single line method, 2X per haploid genome in single platform method and 1X per haploid genome in each application in dual applications method. The means (and the standard deviations) of θ are estimated from 1000 replicates. Error rate is per site.

ISSN: 1471-2164