Table 2. Characterization of SNP data sets.

A benchmark data set for evaluating methods for inversion detection using using SNP data was formed from data for three insect species (D. melanogaster [37, 38], An. gambiae and coluzzii [17, 39]). The chromosome arms were organized into three test cases (negatives, positive drawn from a single population, and positive drawn from multiple populations) based on known inversion genotypes from previous papers. We analyzed SNPs from the 2R chromosome arms of An. gambiae and coluzzii but do not include these data in our benchmark data set since not all inversions were fully characterized. For each chromosome arm, the geographic locations in which the samples were collected, species of the samples, number of samples, inversions identified in these data by the original authors and their frequencies, and the number of SNPs are provideded.

Test Case	Data Source	Location	Species	Chrom.	Samples	Inversions (Frequency)	SNPs
Negative	[37, 38]		D. mel.	3L	192*		896,257
Negative	[39]	BCMT	An. gam. and col.	3L	34		1,329,375
Negative	[17]	B	An. gam. and col.	3L	150		7,449,486
Single	[37, 38]		D. mel.	2L	198	In(2L)t (14.4%)	910,880
Single	[37, 38]		D. mel.	2R	198	In(2R)NS (12.1%)	740,948
Single	[37, 38]		D. mel.	3R	198	In(3R)Mo (18.7%), In(3R)p (7.1%), In(3R)k (8.1%)	884,009
Multiple	[17]	B	An. gam. and col.	2L	150	2La (94.7%)	8,296,600
Multiple	[17]	B	An. gam.	2L	81	2La (90.7%)
Multiple	[39]	BCMT	An. gam. and col.	2L	34	2La (54.4%)
Other	[17]	B	An. gam. and col.	2R	150	2Rb (59.3%)	11,332,702
Other	[17]	B	An. gam.	2R	81	2Rb (82.1%)	11,332,702
Other	[17]	B	An. col.	2R	69	2Rb (31.1%)	11,332,702
Other	[17]	B	An. col.	2L	69	2La (99.3%)	8,296,600

* Inversions were present in only six samples, which we removed; B: Burkina Faso, C: Cameroon, M: Mali, and T: Tanzania