TB-Profiler result

Run: ERR3077958
Summary

Run ID: ERR3077958

Sample name:

Date: 01-04-2023 00:12:38

Number of reads: 400874

Percentage reads mapped: 99.69

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155166 p.Gly316Ser missense_variant 0.25 isoniazid
katG 2155168 p.Ser315Ile missense_variant 1.0 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
gyrB 5107 c.-133C>A upstream_gene_variant 0.12
gyrB 5479 p.Asp80Glu missense_variant 0.11
gyrB 5667 p.Gly143Val missense_variant 0.12
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7577 c.276C>A synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8358 p.Pro353Thr missense_variant 0.22
gyrA 8765 p.Asp488Glu missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491672 p.Val297Ala missense_variant 0.18
mshA 575428 c.81G>T synonymous_variant 0.2
ccsA 620351 p.Arg154His missense_variant 0.25
rpoB 760524 p.Glu240* stop_gained 0.15
rpoB 763173 p.Gln1123Lys missense_variant 0.13
rpoC 763973 p.Glu202* stop_gained 0.13
rpoC 764817 p.Val483Gly missense_variant 0.9
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765869 p.Arg834Ser missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777750 p.Arg244Leu missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406212 p.His377Asn missense_variant 0.14
Rv1258c 1406249 c.1092G>T synonymous_variant 0.18
embR 1417186 c.162C>A synonymous_variant 0.12
embR 1417336 p.Ser4Arg missense_variant 0.11
embR 1417546 c.-199C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472168 n.323G>T non_coding_transcript_exon_variant 0.17
rrl 1474911 n.1254G>T non_coding_transcript_exon_variant 0.17
rrl 1475778 n.2121G>T non_coding_transcript_exon_variant 0.13
rrl 1475828 n.2171G>T non_coding_transcript_exon_variant 0.14
rrl 1476154 n.2497G>T non_coding_transcript_exon_variant 0.2
fabG1 1673674 p.Gln79Lys missense_variant 0.15
fabG1 1673728 p.Leu97Ile missense_variant 0.17
fabG1 1673804 p.Arg122Leu missense_variant 0.18
inhA 1674927 c.726G>A synonymous_variant 0.12
rpsA 1833443 c.-99C>A upstream_gene_variant 0.17
rpsA 1834770 c.1234_1235delGC frameshift_variant 0.13
rpsA 1834835 p.Met432Val missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918568 p.Ala210Glu missense_variant 0.12
ndh 2101715 p.Glu443Gly missense_variant 0.12
katG 2153994 c.2118G>T synonymous_variant 0.15
katG 2154754 p.Ala453Asp missense_variant 0.29
katG 2155695 c.417C>A synonymous_variant 0.13
PPE35 2169024 p.Pro530Gln missense_variant 0.13
Rv1979c 2222889 c.276C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289287 c.-46C>A upstream_gene_variant 0.12
pncA 2289890 c.-649C>A upstream_gene_variant 0.13
kasA 2518052 c.-63G>T upstream_gene_variant 0.2
kasA 2519238 p.Thr375Lys missense_variant 0.18
ahpC 2726269 p.Val26Gly missense_variant 0.22
folC 2746255 p.Asp448Glu missense_variant 0.15
folC 2747353 c.246C>A synonymous_variant 0.22
Rv2752c 3065390 p.Arg268Ser missense_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3073964 p.Leu170Met missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339746 p.Ala210Glu missense_variant 0.17
Rv3083 3449810 p.Phe436Ser missense_variant 0.11
Rv3083 3449849 p.Asp449Gly missense_variant 0.12
Rv3083 3449891 p.Leu463Pro missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474762 c.756G>T synonymous_variant 0.12
whiB7 3568682 c.-3G>T upstream_gene_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612193 c.924C>A synonymous_variant 0.2
fbiA 3640492 c.-51G>T upstream_gene_variant 0.12
fbiB 3640611 c.-924C>A upstream_gene_variant 0.14
fbiA 3640615 p.Leu25Met missense_variant 0.15
fbiA 3640871 p.Ala110Asp missense_variant 0.13
alr 3840208 p.Ala405Ser missense_variant 0.12
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3841554 c.-134T>C upstream_gene_variant 0.18
ddn 3986654 c.-190C>T upstream_gene_variant 0.22
ddn 3986902 p.Trp20Leu missense_variant 0.12
ddn 3986963 c.120C>A synonymous_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039154 c.1551G>T synonymous_variant 0.12
clpC1 4039541 c.1164C>A synonymous_variant 0.22
clpC1 4040608 p.Ile33Val missense_variant 0.12
embC 4240320 p.Gln153Arg missense_variant 0.2
embC 4240926 p.Cys355Tyr missense_variant 0.17
embC 4242114 c.2254delG frameshift_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243217 c.-16C>A upstream_gene_variant 1.0
embA 4244838 p.Leu536Met missense_variant 0.12
embA 4245300 p.Leu690Met missense_variant 0.25
embB 4247253 p.Ser247Leu missense_variant 0.12
embB 4247595 p.Cys361Phe missense_variant 0.22
embB 4247926 c.1413C>A synonymous_variant 0.29
embB 4248234 p.Leu574Pro missense_variant 1.0
embB 4248643 c.2130G>T synonymous_variant 0.15
embB 4248734 c.2221C>A synonymous_variant 0.14
embB 4249028 p.Pro839Thr missense_variant 0.14
aftB 4267573 p.His422Asn missense_variant 0.14
ethA 4326452 p.Ala341Glu missense_variant 0.17
ethR 4326832 c.-717C>A upstream_gene_variant 0.17
ethA 4327117 p.His119Gln missense_variant 0.14
whiB6 4338347 p.Arg59Trp missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 0.93
gid 4408380 c.-178G>T upstream_gene_variant 0.2
gid 4408385 c.-183C>A upstream_gene_variant 0.25