TB-Profiler result

Run: SRR9588018
Summary

Run ID: SRR9588018

Sample name:

Date: 02-08-2023 15:32:20

Number of reads: NA

Percentage reads mapped: NA

Strain: lineage4.4.1.1

Drug-resistance: MDR-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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.1 Euro-American (S-type) S;T None 0.98
lineage4.4.1.1 Euro-American S;Orphans 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 761277 p.Ile491Phe missense_variant 0.96 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Asp missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.95
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763013 c.-357C>G upstream_gene_variant 0.13
rpoC 763028 c.-342T>C upstream_gene_variant 0.17
rpoC 763031 c.-339T>G upstream_gene_variant 0.16
rpoC 763034 c.-336C>G upstream_gene_variant 0.14
rpoC 763070 c.-300T>C upstream_gene_variant 0.13
rpoC 766467 p.Glu1033Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777416 c.1065G>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781808 c.249C>T synonymous_variant 0.14
rpsL 781811 c.252C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674703 c.502T>C synonymous_variant 0.14
inhA 1674708 c.507G>A synonymous_variant 0.14
inhA 1674718 c.517A>C synonymous_variant 0.15
inhA 1674723 c.522C>T synonymous_variant 0.17
inhA 1674738 c.537C>G synonymous_variant 0.17
inhA 1674741 c.540C>T synonymous_variant 0.16
inhA 1674746 p.Tyr182Phe missense_variant 0.16
inhA 1674750 c.549T>C synonymous_variant 0.16
inhA 1674753 c.552G>C synonymous_variant 0.16
inhA 1674756 c.555T>C synonymous_variant 0.16
inhA 1674759 c.558G>C synonymous_variant 0.16
inhA 1674774 c.573A>G synonymous_variant 0.15
inhA 1674780 c.579T>G synonymous_variant 0.18
inhA 1674789 c.588G>C synonymous_variant 0.16
inhA 1674801 c.600T>C synonymous_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2168479 p.Thr712Pro missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518496 c.382C>T synonymous_variant 1.0
Rv2752c 3065023 p.Pro390Leu missense_variant 0.98
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448522 p.Val7Phe missense_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3877986 c.522G>C synonymous_variant 0.14
rpoA 3877989 c.519A>G synonymous_variant 0.16
rpoA 3878001 c.507A>G synonymous_variant 0.17
rpoA 3878022 c.486T>C synonymous_variant 0.14
rpoA 3878028 c.480G>C synonymous_variant 0.14
rpoA 3878031 c.477T>C synonymous_variant 0.15
rpoA 3878040 c.468T>C synonymous_variant 0.14
rpoA 3878043 c.465G>A synonymous_variant 0.14
rpoA 3878055 c.453A>G synonymous_variant 0.14
rpoA 3878058 c.450G>T synonymous_variant 0.14
rpoA 3878061 c.447G>C synonymous_variant 0.14
rpoA 3878067 c.441C>G synonymous_variant 0.14
rpoA 3878070 c.438T>C synonymous_variant 0.13
rpoA 3878076 c.432C>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ubiA 4269299 p.Ile179Val missense_variant 1.0
whiB6 4338487 p.Cys12Ser missense_variant 0.63
whiB6 4338595 c.-75delG upstream_gene_variant 1.0