A method for determining whether a male fetus of a pregnant female has an X-linked mutation, the method comprising: receiving data from a plurality of reactions, each involving one or more nucleic acid molecules from a biological sample, the biological sample including nucleic acid molecules from the pregnant female and from the male fetus, wherein the pregnant female is homozygous for an allele at a locus on the X chromosome, has a mutation of an amplification of the allele on a mutant X chromosome, the mutant X chromosome having a normal copy of the allele at the locus and one or more additional copies of the allele, and has a normal X chromosome having a normal copy of the allele at the locus, wherein the data includes: a first set of quantitative data indicating a first amount of an additional junction created by the one or more additional copies of the allele; and a second set of quantitative data indicating a second amount of a normal junction created by the normal copy of the allele on both X chromosomes; determining a parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts; obtaining a percentage Pf of fetal nucleic acid molecules in the biological sample; calculating a first cutoff value for determining whether the fetus has inherited the mutant X chromosome, wherein the first cutoff value is derived at least from a first proportion of n/(n+2-Pf), where n is the number of additional copies of the allele, n being an integer equal to or greater than one; calculating a second cutoff value for determining whether the fetus has inherited the normal X chromosome, wherein the second cutoff value is derived at least from a second proportion of n(1-Pf)/[n+2-Pf(n+1)]; and comparing the parameter to at least one of the first and second cutoff values to determine a classification of whether the fetus has inherited the mutant X chromosome or the normal X chromosome. receiving data from a plurality of reactions, each involving one or more nucleic acid molecules from a biological sample, the biological sample including nucleic acid molecules from the pregnant female and from the male fetus, wherein the pregnant female is homozygous for an allele at a locus on the X chromosome, has a mutation of an amplification of the allele on a mutant X chromosome, the mutant X chromosome having a normal copy of the allele at the locus and one or more additional copies of the allele, and has a normal X chromosome having a normal copy of the allele at the locus, wherein the data includes: a first set of quantitative data indicating a first amount of an additional junction created by the one or more additional copies of the allele; and a second set of quantitative data indicating a second amount of a normal junction created by the normal copy of the allele on both X chromosomes; a first set of quantitative data indicating a first amount of an additional junction created by the one or more additional copies of the allele; and a second set of quantitative data indicating a second amount of a normal junction created by the normal copy of the allele on both X chromosomes; determining a parameter from the first amount and the second amount, wherein the parameter represents a relative amount between the first and second amounts; obtaining a percentage Pf of fetal nucleic acid molecules in the biological sample; calculating a first cutoff value for determining whether the fetus has inherited the mutant X chromosome, wherein the first cutoff value is derived at least from a first proportion of n/(n+2-Pf), where n is the number of additional copies of the allele, n being an integer equal to or greater than one; calculating a second cutoff value for determining whether the fetus has inherited the normal X chromosome, wherein the second cutoff value is derived at least from a second proportion of n(1-Pf)/[n+2-Pf(n+1)]; and comparing the parameter to at least one of the first and second cutoff values to determine a classification of whether the fetus has inherited the mutant X chromosome or the normal X chromosome.