TB-Profiler result

Run: SRR1002693
Summary

Run ID: SRR1002693

Sample name:

Date: 02-04-2023 14:20:02

Number of reads: 512567

Percentage reads mapped: 97.97

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.98
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.99
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 761130 p.Gly442Trp missense_variant 0.14 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.89 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
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 5846 p.Gly203Trp missense_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8075 p.Glu258Asp missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491135 p.Tyr118Cys missense_variant 0.25
mshA 575469 p.Ala41Val missense_variant 0.4
ccsA 619815 c.-76G>T upstream_gene_variant 0.15
rpoB 761483 c.1677G>T synonymous_variant 0.13
rpoB 761785 p.Thr660Asn missense_variant 0.2
rpoC 762558 c.-812C>A upstream_gene_variant 0.14
rpoC 764202 p.Arg278Leu missense_variant 0.17
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765298 c.1929G>T synonymous_variant 0.18
rpoC 765328 p.His653Gln missense_variant 0.2
rpoC 766206 p.Asp946Gly missense_variant 0.14
rpoC 766219 c.2850C>T synonymous_variant 0.14
rpoC 767284 c.3915C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777157 c.1324C>A synonymous_variant 0.15
mmpL5 777164 c.1317C>T synonymous_variant 0.15
mmpL5 777564 p.Thr306Ser missense_variant 0.17
mmpL5 777912 p.Ala190Asp missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801052 p.Ala82Ser missense_variant 0.29
rplC 801314 p.Arg169Pro missense_variant 0.18
fbiC 1302868 c.-63T>A upstream_gene_variant 0.22
fbiC 1303095 c.165G>A synonymous_variant 1.0
Rv1258c 1406722 p.Gly207Trp missense_variant 0.17
embR 1416222 p.Phe376Leu missense_variant 0.11
embR 1416232 c.1116T>C synonymous_variant 0.11
embR 1417256 p.Gly31Val missense_variant 0.13
atpE 1460895 c.-150G>T upstream_gene_variant 0.15
atpE 1461107 c.63C>A synonymous_variant 0.18
atpE 1461165 c.121C>A synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473275 n.1430C>A non_coding_transcript_exon_variant 0.12
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.13
fabG1 1673346 c.-94C>G upstream_gene_variant 0.23
fabG1 1673349 c.-91G>C upstream_gene_variant 0.21
fabG1 1673357 c.-83G>A upstream_gene_variant 0.19
fabG1 1673359 c.-81T>C upstream_gene_variant 0.19
fabG1 1673361 c.-79C>G upstream_gene_variant 0.2
fabG1 1673380 c.-60C>G upstream_gene_variant 0.36
fabG1 1673467 p.Lys10Glu missense_variant 0.25
inhA 1674372 p.Lys57Asn missense_variant 0.18
inhA 1674859 p.Glu220* stop_gained 0.33
rpsA 1833463 c.-79C>A upstream_gene_variant 0.2
rpsA 1833474 c.-68C>A upstream_gene_variant 0.18
rpsA 1834836 p.Met432Thr missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102070 p.Ala325Thr missense_variant 0.14
ndh 2102113 c.930C>A synonymous_variant 0.13
ndh 2103017 p.Ala9Glu missense_variant 0.17
katG 2155286 p.His276Asn missense_variant 0.18
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156247 c.-136T>C upstream_gene_variant 0.11
PPE35 2167703 p.Leu970Phe missense_variant 0.22
PPE35 2167706 c.2907T>C synonymous_variant 0.22
PPE35 2167745 p.Thr956Arg missense_variant 0.15
PPE35 2169269 c.1344A>G synonymous_variant 0.26
PPE35 2169272 c.1341C>G synonymous_variant 0.25
PPE35 2169278 c.1335T>C synonymous_variant 0.15
PPE35 2169281 c.1332T>G synonymous_variant 0.15
PPE35 2169581 c.1032C>G synonymous_variant 0.16
PPE35 2169587 c.1026G>A synonymous_variant 0.15
PPE35 2169902 p.Leu237Phe missense_variant 0.34
PPE35 2169910 p.Asn235Tyr missense_variant 0.3
PPE35 2170048 p.Leu189Val missense_variant 0.2
PPE35 2170053 p.Thr187Ser missense_variant 0.19
PPE35 2170147 p.Ser156Ala missense_variant 0.21
PPE35 2170159 p.Ala152Ser missense_variant 0.15
PPE35 2170528 p.Ser29Ala missense_variant 0.12
Rv1979c 2222623 p.Gly181Ala missense_variant 0.12
Rv1979c 2222949 c.216C>A synonymous_variant 0.22
Rv1979c 2222982 c.183G>T synonymous_variant 0.2
Rv1979c 2223275 c.-111C>A upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289485 c.-244A>C upstream_gene_variant 0.22
kasA 2518457 p.Gly115Cys missense_variant 0.17
kasA 2518613 p.Pro167Thr missense_variant 0.14
kasA 2518879 c.765A>G synonymous_variant 0.29
kasA 2518882 c.768C>A synonymous_variant 0.29
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2518973 p.Ala287Thr missense_variant 0.14
eis 2714146 p.Val396Ala missense_variant 0.2
eis 2714454 c.879C>A synonymous_variant 0.14
eis 2714810 p.Phe175Leu missense_variant 0.14
folC 2746340 p.Ala420Val missense_variant 1.0
pepQ 2859493 p.Gly309Val missense_variant 0.14
Rv2752c 3064584 c.1608G>T synonymous_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.22
fbiA 3640488 c.-55G>T upstream_gene_variant 0.12
fbiA 3641183 p.Ser214Tyr missense_variant 0.17
fbiB 3641421 c.-114C>A upstream_gene_variant 0.17
alr 3840533 c.888G>T synonymous_variant 0.29
rpoA 3878650 c.-143C>A upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038968 c.1737G>A synonymous_variant 1.0
clpC1 4039313 c.1392C>A synonymous_variant 0.17
clpC1 4039661 c.1044T>C synonymous_variant 0.2
clpC1 4039664 c.1041G>C synonymous_variant 0.18
clpC1 4039667 p.Gln346Tyr missense_variant 0.18
clpC1 4039674 p.Pro344Gln missense_variant 0.22
clpC1 4039676 c.1029G>A synonymous_variant 0.22
clpC1 4039682 c.1023C>T synonymous_variant 0.22
clpC1 4039691 c.1014G>C synonymous_variant 0.18
clpC1 4039714 p.Tyr331His missense_variant 0.18
panD 4043972 c.310C>A synonymous_variant 0.12
embC 4239881 p.Pro7Thr missense_variant 0.2
embC 4240613 p.Leu251Met missense_variant 0.12
embC 4240801 c.939C>T synonymous_variant 0.19
embC 4240803 p.Tyr314Phe missense_variant 0.21
embC 4240960 c.1098G>T synonymous_variant 0.2
embC 4241765 p.Ala635Ser missense_variant 0.14
embC 4241820 p.Ser653* stop_gained 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242704 p.Asp948Asn missense_variant 0.17
embC 4242822 p.Val987Ala missense_variant 0.14
embA 4243418 c.186G>T synonymous_variant 0.33
embA 4243812 c.580C>A synonymous_variant 0.18
embA 4244100 p.Val290Met missense_variant 0.25
embA 4244401 p.Leu390Gln missense_variant 0.18
embB 4247470 c.957T>C synonymous_variant 0.13
embB 4247512 c.999T>C synonymous_variant 0.17
embB 4247516 p.Asn335Asp missense_variant 0.17
embB 4248052 c.1539G>A synonymous_variant 0.25
embB 4249323 p.Ala937Glu missense_variant 0.27
aftB 4268871 c.-35G>T upstream_gene_variant 0.18
ubiA 4269367 p.Ala156Glu missense_variant 0.15
ethR 4326961 c.-588G>C upstream_gene_variant 0.15
ethR 4326964 c.-585G>A upstream_gene_variant 0.15
ethR 4326970 c.-579G>T upstream_gene_variant 0.18
ethA 4327428 p.Gly16Cys missense_variant 0.14
ethR 4327444 c.-105C>A upstream_gene_variant 0.13
ethR 4327816 p.Leu90Ile missense_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407902 p.Leu101Ile missense_variant 0.17
gid 4408156 p.Leu16Arg missense_variant 1.0