Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities

↵Cosmid set 1 GenBank accession nos.: AE000663(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: U88311, AF016443,AF003740, AF016447, AF040643, AF036695, AF040649, AF026210, AF040648,AF040653, AF016678, U97001, AF040654, U80848, AF026211, U97550,AF040655, U41017, AF014940 (cosmids C11D2, C45G7, and R12E2 were not submitted yet). Cosmid set 4 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 4.2 and 8.9 kb long.

Sequencing reactions used Taq polymerase (sets 1 and 2), Sequitherm or TaqFS (set 3), or TaqFS (set 4). Sets one and two were generated almost entirely on ABI 373 sequencing machines running short (34 cm) gels. Set three was generated on ABI 373 machines running short gels (50%) or on ABI 377 machines running short (36 cm) or long (48 cm) gels (21%). (Information about the remaining 29% of the data in this set was not recorded.) Set four was generated mostly on ABI 373 machines running long (48 cm) gels (2.2% of set 4 was sequenced on ABI 377 machines). ABI analysis software was used for lane tracking and processing, and phred v. 0.961028 was used to call bases and assign quality values.