TB-Profiler result

Run: SRR13861308
Summary

Run ID: SRR13861308

Sample name:

Date: 03-04-2023 09:28:32

Number of reads: 2263534

Percentage reads mapped: 75.52

Strain: lineage4.9

Drug-resistance: HR-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
katG 2155411 p.Gly234Glu missense_variant 1.0 isoniazid
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
mshA 576259 c.912C>T synonymous_variant 1.0
ccsA 620690 p.Val267Glu missense_variant 1.0
rpoB 759805 c.-2T>C upstream_gene_variant 1.0
rpoB 761961 p.Pro719Thr missense_variant 1.0
rpoC 764895 p.Ile509Thr missense_variant 1.0
mmpL5 777574 p.Phe303Leu missense_variant 1.0
mmpL5 777578 c.903C>G synonymous_variant 1.0
mmpL5 778982 c.-502A>C upstream_gene_variant 1.0
rplC 801169 p.Lys121* stop_gained 1.0
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 1.0
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.13
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.15
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.15
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.18
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.18
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.18
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.19
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.2
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.2
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.21
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.2
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.2
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.2
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.2
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 0.89
tlyA 1918432 p.Pro165Thr missense_variant 1.0
ndh 2101769 p.Arg425His missense_variant 0.99
katG 2155508 p.Ala202Ser missense_variant 1.0
pncA 2289474 c.-233C>G upstream_gene_variant 1.0
folC 2746862 p.Leu246Arg missense_variant 1.0
folC 2747268 p.Asp111His missense_variant 1.0
Rv2752c 3065109 c.1083A>G synonymous_variant 1.0
fprA 3475241 p.Ala412Gly missense_variant 1.0
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0
clpC1 4038468 p.Asp746Gly missense_variant 1.0
clpC1 4040148 p.Lys186Ile missense_variant 1.0
embC 4240125 p.Cys88Tyr missense_variant 1.0
ethR 4327643 p.Thr32Ile missense_variant 1.0