Table 1 Ten candidate mutations called by GATK (i.e., sites having a read pattern consistent with a genuine single nucleotide or indel mutation) and one confirmed deletion mutation (X 2,693,102) called only by Pindel
Read depthRead depth in mutant individual
LocationDetected by GATK (G) or Pindel (P)Mutation eventOffspring codeFemale parentMale parentOffspring meanWild-type baseMutant baseConfirmed
2L 2,301,848GA→C90283950.43011Yes
2L 5,955,655GC→T88424733.01516Yes
2L 19,399,106GG→T, A (two individuals)74, 88233613.810, 411, 8Yes
2R 6,136,602GG→A89333561.32124Yes
2R 14,887,552GC→A84393264.5459No
2R 16,372,704GC→T89262749.43217Yes
3L 10,514,561G, PDeletion TAAAAATGCTCT94321752.21614Yes
3R 1,431,265GC→T89323444.8336Yes
3R 7,755,276GG→A79265655.35020No
3R 1,2126,610G, PDeletion TCTCCGAAATAGG84283448.72215Yes
X 2,693,102PDeletion TGTT94342159.33912Yes
  • GATK, Genome Analysis Toolkit.