Base-Calling of Automated Sequencer Traces UsingPhred. I. Accuracy Assessment

↵Cosmid set 1 GenBank accession nos. AE00063 (cosmid 0742C), AE000665 (cosmid 82C), U66059 (cosmids A14, G54, K26, K35, AND X21B), AF029308 (cosmids X13A and X224). Cosmid set 2 accession nos.: U23454, U39645, U23529, U39742, U29535, U23518, U29381,U28732, and U29536. Cosmid set 3 accession nos.: AC000099, AC000123,AC000109, AC000110, AC000354, AC000361, AC000362, AC000363, AC000364,AC000355, AC000356, AC000124, AC000125, AC000357, AC000126, AC000127,AC000358, AC000359, AC002495, AC002424, AC000373, AC000365, AC000366,AC000367, AC002113, AC002114, AC002497, AC002083, AC002084, AC000369,AC000370, AC002057, AC000374, AC000371, AC000372, and AC002498.

↵Two of these are cosmid fragments of 4.2 and 8.9 kb long.

All reads were from M13 subclone templates, and almost all were generated in ABI 373 sequencing machines (2.2% of set 3 was sequenced on ABI 377 machines). Cosmid set 1 gels were processed with ABI v. 1.0.x (10.5%), 1.1.x (9.1%), 1.2.x (73.0%), and 2.0.1 (7.3%) analysis software. Cosmid set 2 gels were processed with ABI v. 1.2.x (100.0%) analysis software. Cosmid set 3 gels were processed with ABI version 1.2.x (3.3%), 2.1.x (80.6%), and 3.0.x (16.1%) analysis software. Taq polymerase and short (34 cm) gels were used for cosmid sets 1 and 2. TaqFS polymerase and long (48 cm) gels were used for cosmid set 3.