TB-Profiler result

Run: SRR13861235
Summary

Run ID: SRR13861235

Sample name:

Date: 03-04-2023 09:26:45

Number of reads: 2629915

Percentage reads mapped: 43.88

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
gyrA 7760 c.459C>T synonymous_variant 0.12
mshA 576259 c.912C>T synonymous_variant 1.0
ccsA 620690 p.Val267Glu missense_variant 0.89
rpoB 759805 c.-2T>C upstream_gene_variant 1.0
rpoB 761961 p.Pro719Thr missense_variant 0.88
rpoC 763528 c.159G>A synonymous_variant 0.14
rpoC 764895 p.Ile509Thr missense_variant 0.92
rpoC 766672 c.3303T>C synonymous_variant 0.14
rpoC 766726 c.3357T>C synonymous_variant 0.14
rpoC 766738 c.3369G>T synonymous_variant 0.16
rpoC 766765 c.3396A>C synonymous_variant 0.15
rpoC 766774 c.3405T>C synonymous_variant 0.15
rpoC 766801 c.3432C>A synonymous_variant 0.13
rpoC 766804 c.3435A>G synonymous_variant 0.14
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 0.93
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrl 1474052 n.395G>T non_coding_transcript_exon_variant 0.95
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.13
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.21
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.17
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.15
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.18
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.16
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.16
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.16
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.17
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.16
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.13
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16
rrl 1476479 n.2822T>G non_coding_transcript_exon_variant 0.88
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13
rpsA 1834375 c.834G>A synonymous_variant 0.13
rpsA 1834417 c.876G>C synonymous_variant 0.15
rpsA 1834423 c.882G>C synonymous_variant 0.15
rpsA 1834435 c.894G>C synonymous_variant 0.15
tlyA 1918432 p.Pro165Thr missense_variant 1.0
ndh 2101769 p.Arg425His missense_variant 1.0
katG 2155508 p.Ala202Ser missense_variant 1.0
pncA 2289474 c.-233C>G upstream_gene_variant 1.0
kasA 2518519 c.405G>C synonymous_variant 0.13
kasA 2518540 c.426T>G synonymous_variant 0.14
folC 2746862 p.Leu246Arg missense_variant 1.0
folC 2747268 p.Asp111His missense_variant 0.96
Rv2752c 3065109 c.1083A>G synonymous_variant 0.99
fprA 3475241 p.Ala412Gly missense_variant 1.0
whiB7 3568816 c.-137C>T upstream_gene_variant 1.0
rpoA 3878049 c.459G>C synonymous_variant 0.14
rpoA 3878055 c.453A>G synonymous_variant 0.15
rpoA 3878061 c.447G>C synonymous_variant 0.16
rpoA 3878067 c.441C>G synonymous_variant 0.14
rpoA 3878070 c.438T>C synonymous_variant 0.15
rpoA 3878082 c.426T>C synonymous_variant 0.14
clpC1 4038468 p.Asp746Gly missense_variant 0.89
clpC1 4038536 c.2169C>T synonymous_variant 0.13
clpC1 4039085 c.1620A>G synonymous_variant 0.14
clpC1 4039090 c.1615C>T synonymous_variant 0.14
clpC1 4039097 c.1608G>C synonymous_variant 0.14
clpC1 4039103 c.1602T>C synonymous_variant 0.13
clpC1 4039106 c.1599G>C synonymous_variant 0.14
clpC1 4039112 c.1593C>G synonymous_variant 0.14
clpC1 4039142 c.1563A>G synonymous_variant 0.14
clpC1 4039145 c.1560G>C synonymous_variant 0.14
clpC1 4039169 p.Glu512Asp missense_variant 0.14
clpC1 4039172 c.1533A>G synonymous_variant 0.15
clpC1 4039178 c.1527G>C synonymous_variant 0.14
clpC1 4039183 c.1522T>C synonymous_variant 0.14
clpC1 4040148 p.Lys186Ile missense_variant 0.96
embC 4240125 p.Cys88Tyr missense_variant 0.95
embC 4240726 c.864G>C synonymous_variant 0.13
embC 4240780 c.918T>C synonymous_variant 0.15
embC 4240783 c.921G>C synonymous_variant 0.16
embC 4240789 c.927T>C synonymous_variant 0.16
embB 4248085 c.1572T>C synonymous_variant 0.15
embB 4248097 c.1584C>G synonymous_variant 0.16
embB 4248118 c.1605T>C synonymous_variant 0.13
embB 4248157 c.1644A>G synonymous_variant 0.14
embB 4248208 p.Ser565Arg missense_variant 0.15
embB 4248220 c.1707A>G synonymous_variant 0.17
embB 4248241 c.1728C>T synonymous_variant 0.19
embB 4248265 c.1752C>T synonymous_variant 0.16
embB 4248266 c.1753C>T synonymous_variant 0.17
embB 4248277 c.1764G>C synonymous_variant 0.15
ethR 4327643 p.Thr32Ile missense_variant 0.99