Then I just looked to see what percentage of the reads aligned to these regions:
File %Aligned
antx_M0_A 0.07%
antx_M1_A 0.06%
antx_M2_A 0.06%
antx_M3_A 0.07%
cmnx_M0_C 4.99%
cmnx_M0_E 1.25%
cmnx_M1_C 0.22%
cmnx_M1_E 0.48%
cmnx_M2_C 13.04%
cmnx_M2_E 0.51%
cmnx_M3_C 2.50%
cmnx_M3_E 0.78%
crpx_B1_F 0.12%
crpx_B2_F 0.08%
crpx_M0_E 0.47%
crpx_M1_E 0.43%
crpx_M2_E 0.13%
crpx_M3_E 0.51%
hfqx_M0_D 0.19%
hfqx_M1_D 0.45%
hfqx_M2_D 0.05%
hfqx_M3_D 0.74%
kw20_B1_F 0.81%
kw20_B1_G 0.30%
kw20_B1_H 0.18%
kw20_B2_F 0.32%
kw20_B2_G 0.55%
kw20_B2_H 0.17%
kw20_B3_F 0.31%
kw20_B3_G 0.56%
kw20_B3_H 0.40%
kw20_M0_A 0.04%
kw20_M0_B 0.11%
kw20_M0_C 0.14%
kw20_M1_A 0.11%
kw20_M1_B 0.17%
kw20_M1_C 1.57%
kw20_M2_A 0.10%
kw20_M2_B 0.17%
kw20_M2_C 0.26%
kw20_M3_A 0.07%
kw20_M3_B 0.06%
kw20_M3_C 1.40%
mure_B1_G 0.55%
mure_B1_H 0.26%
mure_B2_G 0.55%
mure_B2_H 0.44%
mure_B3_G 1.16%
mure_B3_H 0.42%
rpod_B1_X 2.60%
rpod_B2_X 0.58%
rpod_B3_X 0.39%
sxy1_B1_G 0.30%
sxy1_B1_H 0.09%
sxy1_B2_G 0.41%
sxy1_B2_H 0.22%
sxy1_B3_G 0.46%
sxy1_B3_H 0.34%
sxyx_B1_G 0.19%
sxyx_B2_G 0.34%
sxyx_M0_A 0.04%
sxyx_M0_B 0.08%
sxyx_M0_D 0.12%
sxyx_M1_A 0.13%
sxyx_M1_B 0.23%
sxyx_M1_D 0.13%
sxyx_M2_A 0.18%
sxyx_M2_B 0.04%
sxyx_M2_D 0.79%
sxyx_M3_A 0.21%
sxyx_M3_B 0.04%
sxyx_M3_D 0.41%
taxx_M0_C 1.28%
taxx_M0_D 0.15%
taxx_M0_E 0.96%
taxx_M1_C 0.27%
taxx_M1_D 0.20%
taxx_M1_E 0.39%
taxx_M2_C 0.36%
taxx_M2_D 0.15%
taxx_M2_E 1.06%
Ignoring the cmnx C replicate that appears to have a lot of rRNA in it, each sample has on average 0.4% rRNA, ranging between 2.60% on the high end and 0.04% on the low end.
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