Next-generation genotyping of hypervariable loci in many individuals of a non-model species: technical and theoretical implications

Table 1 NGS statistics per 454 Titanium 1/8^th lane or individual Ion Torrent PGM run

Run identity	Initial number of reads generated	Initial number of amplicons pooled [number of replicates]	Reads post filtering on Galaxy [% of initial reads]	Final number of amplicons over read threshold of 120 [number of replicates]	Final mean [and range] of read coverage per amplicon
454 Titanium lane 1	138,185	80 [24]	104,937 [75.9 %]	52 [16]	1,448.5 [120–23,492]
454 Titanium lane 2	98,474	102 [21]	78,642 [79.9 %]	30 [0]	1,841.9 [120–11,048]
454 Titanium lane 3	90,355	102 [30]	38,903 [43.1 %]	101 [29]	299.8 [165–471]
454 Titanium lane 4	103,559	115 [19]	29,769 [28.8 %]	81 [13]	210.7 [120–638]
454 Titanium lane 5	108,867	95 [19]	43,921 [40.3 %]	79 [12]	393.8 [120–1,313]
Ion Torrent run 1	607,318	120 [12]	277,195 [45.6 %]	99 [5]	1,885.6 [120–7,190]
Ion Torrent run 2	573,126	120 [16]	198,604 [34.6 %]	99 [8]	1,415.2 [120–5,727]
Ion Torrent run 3	693,065	121 [14]	341,675 [49.3 %]	101 [5]	2,534.6 [120–15,851]
All Runs	2,176,290	855 [155]	930,067 [42.7 %]	642 [88]	1087.8 [120–23,492]

ISSN: 1471-2164