Table 5. Number of single nucleotide and indel polymorphisms after polishing.

	After 4 iterations of Racon			After 6 iterations of Pilon			After 3 iterations of Racon followed by 3 iterations of Pilon
Species	Indels	Homozygous SNPs	Heterozygous SNPs	Indels	Homozygous SNPs	Heterozygous SNPs	Indels	Homozygous SNPs	Heterozygous SNPs
D. ananassae	107,558	36,905	10,643	4,189	294	45,486	1,056	445	10,215
D. biarmipes	256,004	67,310	70,947	9,646	593	123,890	5,341	1,306	73,149
D. bipectinata	310,109	114,548	654,543	71,581	3,173	655,658	59,176	5,056	674,390
D. erecta	209,290	45,382	22,186	2,758	289	37,946	1,150	435	22,179
D. eugracilis	313,426	85,150	712,410	75,480	3,359	708,483	67,204	5,024	740,846
D. mauritiana	131,501	38,401	25,587	3,325	264	39,644	1,954	433	24,885
D. mojavensis	213,411	71,191	36,205	9,772	311	49,328	8,516	755	35,128
D. persimilis	306,714	95,957	103,767	20,144	856	130,685	15,423	1,042	76,465
D. pseudoobscura	266,278	66,505	20,625	5,603	298	54,530	3,265	379	19,349
D. sechellia	214,673	37,740	17,547	2,840	300	34,525	1,420	538	18,117
D. simulans	145,544	39,508	40,197	5,008	349	54,565	3,051	475	40,803
D. triauraria	373,410	171,450	843,725	79,228	3,461	812,711	68,228	5,745	865,396
D. virilis	211,137	71,644	19,972	5,503	265	48,459	4,207	757	20,272
D. willistoni	332,107	110,725	382,209	64,535	2,770	388,208	59,316	5,193	405,046
D. yakuba	283,296	92,344	28,566	4,248	424	59,967	1,839	687	27,336