TB-Profiler result

Run: SRR3732586
Summary

Run ID: SRR3732586

Sample name:

Date: 04-04-2023 05:36:16

Number of reads: 1014647

Percentage reads mapped: 99.51

Strain: lineage4.1.2.1

Drug-resistance: Other

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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 0.99
lineage4.1.2 Euro-American T;H None 1.0
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
folC 2747143 p.Phe152Leu missense_variant 0.14 para-aminosalicylic_acid
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 7713 p.Ala138Ser missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491460 p.Asp226Glu missense_variant 0.2
fgd1 491534 p.Pro251Leu missense_variant 0.4
fgd1 491591 p.Lys270Met missense_variant 0.92
fgd1 491770 p.Pro330Thr missense_variant 0.14
mshA 575372 p.Gly9Arg missense_variant 0.18
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 576025 c.678G>T synonymous_variant 0.12
ccsA 619801 c.-90C>A upstream_gene_variant 0.18
ccsA 619817 c.-74C>T upstream_gene_variant 0.2
rpoB 759719 c.-88C>A upstream_gene_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760454 c.648C>A synonymous_variant 0.12
rpoB 760555 p.Glu250Gly missense_variant 1.0
rpoB 760909 p.Gly368Val missense_variant 0.14
rpoB 760914 p.Arg370Ser missense_variant 0.17
rpoB 762833 p.Ser1009Arg missense_variant 0.14
rpoC 762920 c.-450C>A upstream_gene_variant 0.15
rpoC 764305 p.Met312Ile missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775778 c.2703C>A synonymous_variant 0.2
mmpL5 777417 p.Pro355Gln missense_variant 0.17
mmpL5 777443 c.1038C>T synonymous_variant 0.17
mmpL5 777688 c.793C>T synonymous_variant 0.12
mmpL5 778077 p.Thr135Asn missense_variant 0.17
mmpL5 778351 p.Ala44Thr missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781677 p.Thr40Ala missense_variant 0.14
rplC 801167 p.Gly120Asp missense_variant 0.4
fbiC 1302920 c.-11G>A upstream_gene_variant 1.0
fbiC 1303660 p.Val244Phe missense_variant 0.14
fbiC 1305267 c.2337C>A synonymous_variant 0.13
Rv1258c 1406535 p.Gly269Val missense_variant 0.29
embR 1416300 p.Val350Leu missense_variant 0.17
embR 1416307 c.1041C>T synonymous_variant 0.17
embR 1416659 p.Arg230Leu missense_variant 0.25
rrs 1471649 n.-197C>A upstream_gene_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472342 n.497G>T non_coding_transcript_exon_variant 0.4
fabG1 1673419 c.-21G>T upstream_gene_variant 0.12
fabG1 1673559 p.His40Gln missense_variant 0.12
rpsA 1834216 p.Phe225Leu missense_variant 0.22
rpsA 1834499 p.Leu320Ile missense_variant 0.2
tlyA 1917819 c.-121C>A upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918510 p.Gln191* stop_gained 0.12
ndh 2101910 p.Ala378Val missense_variant 0.33
ndh 2101997 p.Ala349Asp missense_variant 0.17
ndh 2102107 c.936C>A synonymous_variant 0.18
ndh 2102313 p.Gln244* stop_gained 0.22
ndh 2102863 c.180C>T synonymous_variant 0.12
katG 2155324 p.Ala263Glu missense_variant 0.5
katG 2155599 p.Cys171* stop_gained 0.29
katG 2155693 p.Ser140Ile missense_variant 0.25
PPE35 2168729 c.1884C>T synonymous_variant 0.13
Rv1979c 2222156 p.Pro337Thr missense_variant 0.15
Rv1979c 2222771 p.Gln132Lys missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223350 c.-186T>C upstream_gene_variant 0.15
pncA 2288715 p.Arg176His missense_variant 0.2
pncA 2288732 c.510C>T synonymous_variant 0.17
pncA 2289921 c.-680A>G upstream_gene_variant 0.22
pncA 2290172 c.-931T>C upstream_gene_variant 0.2
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714388 c.945C>A synonymous_variant 0.12
eis 2715378 c.-46A>G upstream_gene_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.27
folC 2746277 p.Asp441Gly missense_variant 1.0
folC 2746834 c.765G>A synonymous_variant 0.12
folC 2747159 p.Pro147Leu missense_variant 0.13
folC 2747250 p.Pro117Thr missense_variant 0.17
pepQ 2859330 c.1089C>A synonymous_variant 0.13
pepQ 2859422 p.Arg333Ser missense_variant 0.13
pepQ 2860393 p.Lys9Arg missense_variant 0.2
ribD 2987475 p.Leu213Met missense_variant 0.18
Rv2752c 3065223 c.969T>C synonymous_variant 0.15
Rv2752c 3066254 c.-63G>T upstream_gene_variant 0.14
thyA 3074196 c.276G>T synonymous_variant 0.18
thyA 3074610 c.-139G>T upstream_gene_variant 0.5
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.2
Rv3083 3448559 p.Thr19Met missense_variant 0.12
Rv3083 3448707 c.204G>T synonymous_variant 0.2
Rv3083 3449145 c.642G>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474746 p.Gln247Arg missense_variant 0.14
fprA 3475294 p.Glu430* stop_gained 0.14
whiB7 3568660 p.Pro7His missense_variant 0.18
Rv3236c 3613309 c.-193G>T upstream_gene_variant 0.25
fbiB 3641954 c.420C>A synonymous_variant 0.12
fbiB 3642189 p.Gly219Trp missense_variant 0.18
rpoA 3877719 p.Cys263* stop_gained 0.13
ddn 3987021 c.178C>A synonymous_variant 0.18
clpC1 4039029 p.Lys559Met missense_variant 0.2
clpC1 4039721 p.Tyr328* stop_gained 0.15
panD 4044007 p.Thr92Lys missense_variant 0.29
embC 4240317 p.Cys152Phe missense_variant 0.17
embC 4240458 p.Gly199Val missense_variant 0.13
embC 4241248 c.1386G>A synonymous_variant 0.18
embC 4241578 c.1716G>A synonymous_variant 0.17
embC 4242047 p.Ser729Pro missense_variant 0.15
embA 4242374 c.-859C>A upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245800 p.Trp856Cys missense_variant 0.13
embB 4245932 c.-582C>A upstream_gene_variant 0.15
embA 4246311 p.Gly1027Cys missense_variant 0.2
embB 4247648 p.Ala379Ser missense_variant 0.12
aftB 4267303 p.Asn512Asp missense_variant 0.15
aftB 4267418 c.1419G>T synonymous_variant 0.17
aftB 4268243 c.594C>A synonymous_variant 0.2
ubiA 4270005 c.-172C>A upstream_gene_variant 0.15
ethA 4326289 c.1185C>A synonymous_variant 1.0
ethA 4326891 p.Ala195Ser missense_variant 0.29
ethA 4327121 p.Val118Ala missense_variant 0.25
ethA 4327674 c.-201C>T upstream_gene_variant 0.25
ethR 4328082 p.Met178Ile missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408061 p.His48Asn missense_variant 0.12