Table 2.

Quality assessment of assembled genomes.

Strain	101/04	2322	VV9-09	491771	VV 4-03	BAA87a	VVyb1a
No. of reads	9,786,036	9,150,870	7,465,222	7,291,670	7,944,338	NA	NA
Average length – contigs (bp)	14,853	12,811	13,463	9,774	11,454	23,531	41,029
No. contigs (≥0 bp)	370	413	391	543	460	218	140
No. contigs (≥1000 bp)	63	78	177	200	190	187	115
GC (%)	46.32	46.4	46.42	46.43	46.42	46.49	46.73
N50	506,351	324,391	54,238	57,095	57,166	52,210	230,903
N75	143,535	161,992	33,564	34,718	33,212	32,756	109,426
No. of fully unaligned contigs	133	162	101	175	139	68	43
Fully unaligned length (bp)	170,338	152,003	326,751	390,311	369,492	284,904	226,696
No. mismatches per 100 kbpb	3717.52	3753.33	3024.61	3013.1	3022.73	3019.71	2875.88
No. indels per 100 kbpc	73.28	93.49	77.05	80.98	77.7	80.33	59.75
Genome fraction (%)d	63.6	61.4	79.8	78.9	79.4	79.9	79.3
No. predicted genes (≥0 bp)	5017	4836	4961	5068	5026	4907	5291
No. predicted genes (≥300 bp)	4380	4255	4206	4264	4196	4279	4699
No. predicted genes (≥1500 bp)	752	722	719	713	714	680	806
No. predicted genes (≥3000 bp)	85	84	73	71	72	63	78

N50 is the length for which the collection of all contigs of that length or longer covers at least half an assembly. N75, defined similarly to N50, with 75% instead of 50%.

^aStrains sequenced by others (Danin-Poleg et al., 2013; Phillips et al., 2014).

^bThe average number of mismatches per 100,000 aligned bases. True SNPs and sequencing errors are not distinguished and are counted equally.

^cThe average number of indels per 100,000 aligned bases. Several consecutive single nucleotide indels are counted as one indel.

^dPercentage of aligned bases in the reference.