Table 3. Sequencing depth and reference coverage.

Chromosome level descriptions of the average number of reads covering each basepair, as well as the percentage of basepairs of the reference covered. The highest value for a chromosome is accented with bold text, while the lowest value is accented with italic text. Winnowmap2 abbreviated as WM2.

	SMRT-CCS											Nanopore
	Mean depth (x-depth)					Coverage of basepairs (%)						Mean depth (x depth)				Coverage of basepairs (%)
	LRA	Minimap2	NGMLR	WM2		LRA	Minimap2	NGMLR	WM2			Minimap2	NGMLR	WM2		Minimap2	NGMLR	WM2
chr1	19.0627	20.0049	17.9711	20.002		91.7893	92.3244	91.1358	92.3622		chr1	37.7867	33.3715	37.4783		92.4802	91.4793	92.4861
chr2	20.0613	20.1343	19.9393	20.1463		98.7397	98.8041	98.707	98.6286		chr2	40.1079	36.3557	39.497		99.0601	98.8241	98.8272
chr3	20.1303	20.5557	20.0446	20.3575		98.984	99.5552	98.7438	99.5645		chr3	37.7894	36.5499	39.9339		99.773	98.8066	99.767
chr4	20.4284	20.7247	20.1254	21.8975		99.1528	99.0963	98.6843	99.2809		chr4	39.8297	36.1401	39.6729		99.4841	98.7817	99.5176
chr5	20.0292	20.3439	19.7821	20.0655		98.2323	98.1787	97.6187	98.2961		chr5	37.1564	35.9384	37.17		98.5218	98.0472	98.5096
chr6	19.9858	20.4916	19.9745	20.4963		98.795	99.0781	98.674	99.2314		chr6	37.4983	36.4317	38.3408		99.4746	98.9018	99.4822
chr7	19.5124	19.7661	19.3123	19.7686		98.1498	99.2092	97.7858	98.9308		chr7	37.5093	35.7748	37.3072		99.6968	98.4965	99.6698
chr8	20.0067	20.279	19.7645	20.272		98.5302	99.2526	98.1774	99.0982		chr8	37.2117	35.8164	37.4528		99.6024	98.4431	99.6027
chr9	17.085	17.2704	16.5087	17.2736		86.2352	86.2731	85.4122	86.3347		chr9	33.7857	31.5634	33.62		87.3625	86.6206	87.4715
chr10	19.8087	20.0826	19.4999	20.5247		98.2398	98.8789	98.1124	98.8153		chr10	37.9547	35.509	37.9365		99.3546	98.2053	99.3873
chr11	19.5361	19.8058	19.4349	19.8105		98.0161	99.1255	98.1379	98.264		chr11	37.5146	35.9223	37.282		99.562	98.5893	99.0318
chr12	19.6294	19.9493	19.6137	19.9618		98.3953	99.548	98.151	99.3563		chr12	37.9345	36.4544	37.6064		99.8008	98.397	99.7298
chr13	17.5257	18.1764	16.9585	17.6178		85.2628	85.3114	84.1626	85.3793		chr13	32.6205	30.5633	32.35		85.6486	84.3648	85.6546
chr14	16.815	16.8162	16.6225	16.9593		82.5962	82.5668	82.5949	82.5858		chr14	31.2147	30.4015	31.9599		82.5971	82.5928	82.5975
chr15	16.0919	16.3256	15.7467	16.3303		80.7849	81.7561	80.0048	81.9674		chr15	32.9232	30.434	32.7613		82.7815	80.8381	82.8274
chr16	18.4585	19.5281	18.1335	19.4345		89.1223	90.0939	87.9862	90.1285		chr16	36.9247	34.5339	37.2781		90.5049	88.4413	90.5183
chr17	18.0451	18.8278	18.0519	18.7767		95.1484	97.5541	94.7803	95.9119		chr17	37.2793	35.2194	36.9045		97.3704	95.1519	98.046
chr18	19.4328	19.7389	18.8198	19.7815		96.004	98.3045	94.3649	97.8677		chr18	36.8051	34.2153	36.5148		99.3802	94.1824	99.0731
chr19	16.8558	16.8674	16.5895	16.8926		95.0649	95.0588	94.9148	95.0692		chr19	36.3404	33.9213	39.4614		95.1037	95.0137	95.1095
chr20	19.34	20.0554	19.0343	20.1369		96.0126	98.1195	95.5606	98.0231		chr20	39.3238	35.3079	39.1318		99.1143	96.3336	99.1551
chr21	18.0549	18.4984	16.8995	18.2805		80.4792	80.4144	78.9093	80.16		chr21	35.4168	30.0951	34.298		81.3939	80.763	81.2955
chr22	13.9854	14.0173	13.3346	17.4726		72.7139	72.6378	72.5114	72.7444		chr22	32.7008	25.9485	31.1753		72.9147	72.9092	72.9018
chrX	9.8603	9.97983	9.73401	9.98727		97.639	97.9196	96.4952	98.0195		chrX	36.1372	33.9833	35.6273		99.1734	97.0137	98.9417
chrY	7.94848	8.21933	3.85465	8.37289		40.9697	40.9213	37.9947	40.8261		chrY	1.8305	0.501775	1.3745		3.1548	4.9006	2.37513
chrM	1010.03	1203.88	1203.67	1202.19		100	100	100	100		chrM	11954.1	11413.1	11685.6		100	100	100