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Table 4 Comparison of Drosophila melanogaster protein recovery for genes in THO complex

From: SAUTE: sequence assembly using target enrichment

Gene and isoform Method/Reads SRR10541157 SRR10541159 SRR10541107 SRR10541200 SRR10541164
Read bases (Gb) 2.51 2.78 2.95 3.47 4.49
tho2 isoform A SAUTE w/ D. mel 1..1527, 100% Full, 100% Full, 100% Full, 100% Full, 100%
SAUTE w/ D. inn 1..1527, 100% Full, 100% Full, 100% Full, 100% Full, 100%
rnaSPAdes Not found Not found Not found Not found Not found
Trinity Not found Full, 100% Not found Not found Not found
Clust w/ D. mel Not found Not found Not found Not found Full, 100%
Clust w/ D. inn Not found Not found Not found Not found Not found
tho2 isoform B SAUTE w/ D. mel Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
SAUTE w/ D. inn Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
rnaSPAdes Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
Trinity Full, 100% 1..1528, 100% Full, 100% Full, 100% Full, 100%
Clust w/ D. mel Full, 100% Full, 100% Full, 100% Full, 100% Not found
Clust w/ D. inn Not found Not found Not found Not found Not found
tho2 isoform C SAUTE w/ D. mel Not found Not found Not found Not found 1..1539, 100%
SAUTE w/ D. inn Not found Not found Not found Not found 1..1539, 100%
rnaSPAdes Not found Not found Not found Not found Not found
Trinity Not found Not found Not found Not found Not found
Clust w/ D. mel Not found Not found Not found Not found Not found
Clust w/ D. inn Not found Not found Not found Not found Not found
thoc5 SAUTE w/ D. mel Full, 100% Full, 100% Full, 100% Full, 99.5% Full, 100%
SAUTE w/ D. inn Full, 100% Full, 100% Full, 100% Full, 99.5% Full, 100%
rnaSPAdes Full, 99.8% Full, 100% Full, 100% Full, 99.5% Full, 99.7%
Trinity Full, 99.8% Full, 100% Full, 100% Full, 99.5% Full, 99.7%
Clust w/ D. mel Full, 100% Full, 100% Full, 100% Full, 99.5% Full, 99.7%
Clust w/ D. inn Full, 100% Full, 99.8% Full, 100% Full, 99.5% Full, 100%
thoc6 SAUTE w/ D. mel Full, 99.7% Full, 99.7% Full, 100% Full, 99.7% Full, 99.7%
SAUTE w/ D. inn Full, 99.7% Full, 99.7% Full, 100% Full, 99.7% Full, 99.7%
rnaSPAdes Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7%
Trinity Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7%
Clust w/ D. mel Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7%
Clust w/ D. inn Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7% Full, 99.7%
Hpr 1 SAUTE w/ D. mel Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
SAUTE w/ D. inn Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
rnaSPAdes Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
Trinity Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
Clust w/ D. mel Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
Clust w/ D. inn Full, 100% Full, 100% Full, 100% Full, 100% Full, 100%
thoc7 isoform A SAUTE w/ D. mel Not found Not found 24..288, 100% 10..288, 100% Not found
SAUTE w/ D. inn Not found Not found 24..288, 100% 10..288, 100% Not found
rnaSPAdes Not found Not found Full, 99.7% 10..288, 100% Not found
Trinity Not found Not found Full, 99.7% 10..288, 100% Not found
Clust w/ D. mel Not found Not found Full, 99.7% 10..288, 100% Not found
Clust w/ D. inn Not found Full, 99.7% 12..288, 99.6% 10..288, 100% Not found
thoc7 isoform B SAUTE w/ D. mel Not found Not found Not found 10..287, 100% Not found
SAUTE w/ D. inn Not found Not found Not found Not found Not found
rnaSPAdes Not found Not found Not found Not found Not found
Trinity Not found Not found Not found Not found Not found
Clust w/ D. mel Not found Not found Not found Not found Not found
Clust w/ D. inn Not found Not found Not found Not found Not found
  1. SAUTE_PROT low (SAUTE) and CLUSTER (Clust) used proteins in Table 3 for Drosophila melanogaster (D. mel) and Drosophila innubila (D. inn) as targets. Cells in bold and highlighted in yellow show cases where the D. mel protein is recovered perfectly and there is at least one method that does not recover it perfectly. Proteins recovered as full length are marked as ’Full’; otherwise, coordinates on D. mel protein recovered are provided