TB-Profiler result

Run: SRR13861703
Summary

Run ID: SRR13861703

Sample name:

Date: 03-04-2023 09:38:27

Number of reads: 331214

Percentage reads mapped: 16.58

Strain: lineage4.9

Drug-resistance: RR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs
rpoB 761131 p.Gly442Glu missense_variant 0.31 rifampicin
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction
gyrB 5210 c.-30C>G upstream_gene_variant 1.0
ccsA 620747 p.Gly286Val missense_variant 1.0
rpoB 761126 c.1320G>T synonymous_variant 0.31
rpoB 761129 c.1323G>C synonymous_variant 0.31
rpoB 761133 p.Leu443Ile missense_variant 0.31
rpoB 761150 c.1344A>C synonymous_variant 0.31
rpoB 761151 p.Leu449Val missense_variant 0.31
rpoB 761156 c.1350G>C synonymous_variant 0.31
rpoB 761162 c.1356G>C synonymous_variant 0.31
rpoB 761165 c.1359G>C synonymous_variant 0.31
rpoB 761168 c.1362C>G synonymous_variant 0.31
rpoB 761178 p.Ser458Thr missense_variant 0.23
rpoB 761192 c.1386C>G synonymous_variant 0.29
rpoB 761195 c.1389G>C synonymous_variant 0.29
rpoB 761196 p.Leu464Phe missense_variant 0.29
rpoB 761204 c.1398C>T synonymous_variant 0.31
rpoB 761207 c.1401C>T synonymous_variant 0.29
rpoB 761213 c.1407G>A synonymous_variant 0.29
rpoB 761220 p.Ser472Thr missense_variant 0.29
rpoB 761234 c.1428G>C synonymous_variant 0.29
rpoB 761235 p.Met477Val missense_variant 0.29
mmpS5 778670 p.Gln79Pro missense_variant 1.0
rpsL 781927 p.Lys123Met missense_variant 1.0
fbiC 1304806 p.Pro626Thr missense_variant 1.0
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.31
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.33
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.31
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.31
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.31
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.29
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.29
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.31
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.29
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.29
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.31
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.31
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.29
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.29
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.29
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.29
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.27
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.17
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.17
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.87
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.88
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.88
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.88
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.88
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.88
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.9
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.9
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.9
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.88
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.87
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.87
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.87
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.87
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.87
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.87
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.86
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.86
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.85
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.83
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.53
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.17
rpsA 1834614 p.Ile358Ser missense_variant 1.0
PPE35 2168978 c.1635A>C synonymous_variant 0.33
PPE35 2169834 p.Gly260Val missense_variant 1.0
kasA 2518887 p.Gly258Val missense_variant 1.0
eis 2715520 c.-188C>T upstream_gene_variant 1.0
ahpC 2725916 c.-277_-276insA upstream_gene_variant 1.0
pepQ 2859750 c.669C>T synonymous_variant 1.0
embA 4245437 p.Met735Ile missense_variant 1.0
embB 4246876 c.363G>A synonymous_variant 1.0
embB 4248914 p.Ala801Thr missense_variant 1.0
ubiA 4269329 p.Lys169Glu missense_variant 1.0
ethA 4326973 p.Trp167Cys missense_variant 1.0
ethA 4327382 p.Ser31Ile missense_variant 1.0