TB-Profiler result

Run: SRR3732574

Summary

Run ID: SRR3732574

Sample name:

Date: 04-04-2023 05:35:51

Number of reads: 1239102

Percentage reads mapped: 99.57

Strain: lineage4.1.2.1

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;H None 0.99
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2154597 p.Trp505* stop_gained 0.22 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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7890 p.Leu197Met missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9405 p.Gly702Cys missense_variant 0.14
fgd1 491042 p.Ala87Val missense_variant 0.13
fgd1 491290 p.Val170Leu missense_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575776 p.His143Gln missense_variant 0.12
mshA 576091 c.744C>A synonymous_variant 0.2
ccsA 620260 p.Ala124Ser missense_variant 0.13
ccsA 620494 c.604C>A synonymous_variant 0.14
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760153 p.Cys116Phe missense_variant 0.11
rpoB 760646 c.840C>A synonymous_variant 0.2
rpoB 760866 p.Gly354Cys missense_variant 0.14
rpoB 761401 p.Arg532His missense_variant 0.25
rpoC 762383 c.-987C>T upstream_gene_variant 0.13
rpoB 762464 p.Lys886Asn missense_variant 0.2
rpoB 762582 p.Leu926Met missense_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765379 c.2010G>T synonymous_variant 0.12
rpoC 767282 p.Val1305Phe missense_variant 0.13
rpoC 767293 p.Asp1308Glu missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775758 p.Thr908Ile missense_variant 0.18
mmpL5 776344 p.Gly713Trp missense_variant 0.14
mmpL5 777284 c.1197C>A synonymous_variant 0.22
mmpL5 778957 c.-477C>T upstream_gene_variant 0.29
mmpR5 779380 p.Gln131Lys missense_variant 0.2
mmpS5 779515 c.-610C>A upstream_gene_variant 0.29
rpsL 781385 c.-175C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303133 p.Ala68Gly missense_variant 0.13
fbiC 1303510 p.Gly194Cys missense_variant 0.22
fbiC 1304512 p.Val528Ile missense_variant 0.18
fbiC 1304911 p.Leu661Met missense_variant 0.2
embR 1416855 p.Ala165Ser missense_variant 0.15
atpE 1461216 p.Gly58Cys missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674228 c.27G>T synonymous_variant 0.29
inhA 1674246 c.45C>A synonymous_variant 0.33
inhA 1674453 c.252G>A synonymous_variant 0.2
rpsA 1834219 c.678C>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101976 p.Pro356Leu missense_variant 0.12
katG 2154595 p.Glu506Val missense_variant 0.22
katG 2154782 p.Ala444Ser missense_variant 0.12
katG 2155417 p.Pro232Gln missense_variant 0.14
PPE35 2168416 p.Gly733Trp missense_variant 0.25
PPE35 2170206 p.Ala136Asp missense_variant 0.12
Rv1979c 2222154 c.1011G>A synonymous_variant 0.33
Rv1979c 2222211 c.954G>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289337 c.-96T>C upstream_gene_variant 0.1
pncA 2289980 c.-739G>T upstream_gene_variant 0.25
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518147 c.33C>T synonymous_variant 0.22
kasA 2518315 c.201G>T synonymous_variant 0.15
eis 2714658 c.675G>T synonymous_variant 0.15
ahpC 2726150 c.-43G>A upstream_gene_variant 0.14
ahpC 2726774 c.582G>T synonymous_variant 0.13
folC 2747334 p.Leu89Val missense_variant 0.1
pepQ 2859408 c.1011C>A synonymous_variant 0.12
pepQ 2859933 c.486C>T synonymous_variant 0.13
thyA 3073978 c.493delC frameshift_variant 0.13
thyA 3074272 p.Ser67Tyr missense_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448655 p.Pro51Gln missense_variant 0.18
Rv3083 3449075 p.Thr191Asn missense_variant 0.17
Rv3083 3449785 p.Asp428Tyr missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474027 c.21C>A synonymous_variant 0.29
fprA 3474099 p.Asp31Glu missense_variant 0.2
fprA 3474112 p.Val36Ile missense_variant 0.2
fprA 3474293 p.Arg96Leu missense_variant 0.18
fprA 3474645 c.639C>T synonymous_variant 0.22
fprA 3474689 p.Ala228Glu missense_variant 0.15
whiB7 3568430 p.Gly84* stop_gained 0.15
fbiA 3641210 p.Ile223Thr missense_variant 0.13
fbiB 3642302 c.768C>A synonymous_variant 0.13
alr 3840636 p.Pro262Gln missense_variant 0.14
rpoA 3877475 c.1032dupC frameshift_variant 0.15
rpoA 3877947 c.561C>A synonymous_variant 0.14
rpoA 3877951 p.Arg186Leu missense_variant 0.14
rpoA 3878302 p.Val69Asp missense_variant 0.14
ddn 3986820 c.-24C>A upstream_gene_variant 0.14
clpC1 4038410 p.Asp765Glu missense_variant 0.11
clpC1 4040136 p.Val190Ala missense_variant 0.14
clpC1 4040377 c.328C>T synonymous_variant 0.12
clpC1 4040658 p.Ala16Asp missense_variant 0.17
embC 4240821 p.Pro320His missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4244600 c.1368G>T synonymous_variant 0.12
embA 4244607 p.Leu459Met missense_variant 0.12
embA 4245198 p.Leu656Ile missense_variant 0.33
embA 4245816 p.Arg862Ser missense_variant 0.14
embA 4246159 p.Pro976Leu missense_variant 0.18
embB 4246744 c.231C>A synonymous_variant 0.15
embB 4248219 p.Gly569Val missense_variant 0.13
embB 4248320 p.Gly603Trp missense_variant 0.13
embB 4248735 p.Arg741Leu missense_variant 0.12
embB 4248841 c.2328C>A synonymous_variant 0.12
aftB 4268140 p.Gly233* stop_gained 0.13
aftB 4268250 p.Ala196Glu missense_variant 0.18
aftB 4268451 p.Pro129Leu missense_variant 0.13
ubiA 4269097 p.Ser246Tyr missense_variant 0.15
ubiA 4269790 p.Ala15Asp missense_variant 0.17
ethR 4327207 c.-342C>A upstream_gene_variant 0.17
whiB6 4338503 p.Ala7Ser missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408011 c.192G>T synonymous_variant 0.12