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Figure S1. Reproducibility analysis for four duplicate sequence libraries, A, B, C, and D, and example Significance Analysis of Microarrays (SAM) plotsheet.

Figure S2. Rarefaction analyses for fungi in dust samples collected from homes during the rainy season and homes with and without visible mold growth.

Figure S3. Rarefaction analyses for fungi in dust samples collected from homes with and without a water leak and with and without peeling paint as moisture indicators.

Figure S4. Rarefaction analyses for fungi in dust samples collected from homes with and without the maximum moisture content of any wall recorded above a threshold.

Figure S5. Pearson correlation coefficients and graphs of maximum moisture content of any wall in the home compared to the number of Cryptococcus species in floor dust.

Figure S6. Pearson correlation coefficient and graph of the number of total fungal OTUs compared to the number of Cryptococcus species in floor dust.

Figure S7. The most abundant species (>1%) among all samples analyzed by average relative abundance in case and control homes.

Figure S8. Relative abundance of fungal sequences in case and control homes by rank of class.

Figure S9. Principal coordinate analysis graphs of fungal diversity in floor dust.

Figure S10. Principal coordinate analysis graphs of fungal diversity in floor dust.

Table S1. List of identified fungal species in all homes with at least 20 sequences total from all samples in order from most abundant to least abundant by number of sequences identified.

Table S2. Additional fungal α diversity measures calculated in QIIME with the mean values in asthma case and control homes and P-values.

Table S3. Odds ratios for low fungal diversity with classes and prevalent genera in asthma case versus control homes.

Table S4. Summary of moisture indicators found in homes and unadjusted odds ratios for moisture indicators and childhood asthma.

Table S5. Odds ratios for qPCR measurements in 13 asthma case versus 28 control homes.

Table S6. Odds ratios for fungal species abundances in asthma case versus control homes.

Table S7. Odds ratios for fungal genus abundances in asthma case versus control homes.

Table S8. Odds ratios for fungal class abundances in asthma case versus control homes.

Table S9. Odds ratios for statistically significant fungal species, genera, or classes in homes with and without two or more qualitative moisture indicators, visible mold growth, measured moisture at three threshold values (17, 21, and 24) and case/control homes.

Data S1. Methods.

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