TB-Profiler result

Run: SRR6982173
Summary

Run ID: SRR6982173

Sample name:

Date: 04-04-2023 18:29:33

Number of reads: 335972

Percentage reads mapped: 99.53

Strain: lineage4.8.1;lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.86
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.05
lineage4.3.2 Euro-American (LAM) LAM3 None 0.85
lineage4.8.1 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.05
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.83
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
embB 4247495 p.Asp328Tyr missense_variant 0.14 ethambutol
ethA 4326008 c.1465delG frameshift_variant 0.17 ethionamide, 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 5105 c.-135G>C upstream_gene_variant 0.1
gyrB 5520 p.Pro94Leu missense_variant 0.78
gyrA 7222 c.-80C>T upstream_gene_variant 0.93
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.86
gyrA 9304 p.Gly668Asp missense_variant 0.94
fgd1 491249 p.Arg156Gln missense_variant 0.18
ccsA 620068 p.Thr60Ala missense_variant 0.12
rpoB 759619 c.-188C>G upstream_gene_variant 0.14
rpoB 760187 c.383delT frameshift_variant 0.12
rpoB 760379 c.574_575delAC frameshift_variant 0.13
rpoB 761377 p.Tyr524Cys missense_variant 0.11
rpoB 763008 p.Trp1068Arg missense_variant 0.17
rpoC 763802 p.His145Tyr missense_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.84
rpoC 765727 c.2358T>C synonymous_variant 0.18
rpoC 766471 c.3102G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776862 p.His540Leu missense_variant 0.11
mmpS5 778889 p.Lys6Arg missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302794 c.-137A>G upstream_gene_variant 0.15
fbiC 1302863 c.-68A>G upstream_gene_variant 0.11
fbiC 1303904 p.Leu325Pro missense_variant 0.12
Rv1258c 1406150 c.1191G>A synonymous_variant 0.15
embR 1417164 p.Glu62Lys missense_variant 0.25
embR 1417450 c.-103C>T upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.67
rrs 1472550 n.705G>T non_coding_transcript_exon_variant 0.13
rrs 1472910 n.1065G>A non_coding_transcript_exon_variant 0.14
inhA 1673442 c.-760G>A upstream_gene_variant 0.12
fabG1 1673587 p.Gly50* stop_gained 0.2
inhA 1674401 p.Asn67Ser missense_variant 0.11
rpsA 1833512 c.-30A>T upstream_gene_variant 0.15
rpsA 1834152 p.Asn204Ser missense_variant 0.12
rpsA 1834876 c.1335G>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918509 c.570T>A synonymous_variant 0.17
katG 2155119 c.993T>C synonymous_variant 0.17
katG 2155506 c.606C>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289737 c.-496A>G upstream_gene_variant 0.14
kasA 2518726 c.612G>T synonymous_variant 0.17
kasA 2518734 p.Ile207Thr missense_variant 0.15
ahpC 2726370 p.Val60Leu missense_variant 0.17
ahpC 2726529 p.Asp113Tyr missense_variant 0.14
pepQ 2859442 p.Pro326His missense_variant 0.11
Rv2752c 3065263 c.926_928dupGCG conservative_inframe_insertion 0.12
Rv2752c 3067074 c.-883C>G upstream_gene_variant 0.2
thyA 3073868 p.Thr202Ala missense_variant 0.92
thyA 3073930 p.Tyr181Cys missense_variant 0.13
ald 3086782 c.-38T>C upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 0.67
ald 3087226 p.Val136Ala missense_variant 0.14
ald 3087570 p.Ser251Pro missense_variant 0.18
ald 3087902 c.1083G>A synonymous_variant 0.22
fbiD 3339040 c.-78T>C upstream_gene_variant 0.12
fbiD 3339266 p.Ala50Glu missense_variant 0.13
fbiD 3339457 c.342delA frameshift_variant 0.33
Rv3083 3448466 c.-38G>C upstream_gene_variant 0.2
fprA 3473832 c.-175T>C upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.88
fprA 3474256 p.Val84Ile missense_variant 0.15
fprA 3474605 c.600delA frameshift_variant 0.25
fprA 3474847 p.Lys281Glu missense_variant 0.15
fbiA 3641309 p.Ala256Val missense_variant 0.12
fbiB 3642874 p.Leu447Arg missense_variant 0.33
ddn 3986845 c.2T>C start_lost 0.15
ddn 3986869 p.Leu9Pro missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 0.93
clpC1 4038806 p.Glu633Asp missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243782 p.Gly184Trp missense_variant 0.11
embA 4245993 p.Ala921Thr missense_variant 0.2
embA 4246291 p.Leu1020Pro missense_variant 0.12
embB 4246694 c.186delG frameshift_variant 0.11
embB 4247352 p.Asp280Gly missense_variant 0.11
embB 4247702 p.Pro397Ser missense_variant 0.13
embB 4248740 p.Phe743Leu missense_variant 0.15
embB 4249291 c.2780delA frameshift_variant 0.11
aftB 4268050 p.Pro263Ser missense_variant 0.14
aftB 4268182 p.Phe219Leu missense_variant 0.12
aftB 4268293 p.Ser182Gly missense_variant 0.14
ubiA 4269339 c.494delG frameshift_variant 0.12
ethA 4326007 c.1467T>C synonymous_variant 0.17
ethA 4326462 p.Ile338Val missense_variant 0.13
ethR 4326565 c.-984C>T upstream_gene_variant 0.14
ethR 4326649 c.-900C>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407766 p.Thr146Lys missense_variant 0.1
gid 4408156 p.Leu16Arg missense_variant 0.83