TB-Profiler result

Run: ERR3077966

Summary

Run ID: ERR3077966

Sample name:

Date: 01-04-2023 00:12:56

Number of reads: 577267

Percentage reads mapped: 99.26

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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 761139 p.His445Tyr missense_variant 0.15 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.8 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.75 isoniazid
embB 4248002 p.Gln497Lys missense_variant 0.13 ethambutol
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 5101 c.-139G>T upstream_gene_variant 0.12
gyrB 5620 c.381G>T synonymous_variant 0.12
gyrB 5861 c.622C>T synonymous_variant 0.13
gyrA 7018 c.-284G>T upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7563 p.Gly88Ser missense_variant 0.17
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7605 p.Pro102Ala missense_variant 0.14
gyrA 8445 p.Arg382Ser missense_variant 0.17
gyrA 9151 p.Tyr617Cys missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9603 p.Val768Phe missense_variant 0.15
fgd1 491190 c.408G>T synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491774 p.Arg331Met missense_variant 0.13
mshA 576238 c.891G>T synonymous_variant 0.13
mshA 576380 p.Leu345Val missense_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761053 p.Pro416Leu missense_variant 0.17
rpoB 761063 c.1257C>A synonymous_variant 0.18
rpoB 761332 p.Pro509Leu missense_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763098 p.Glu1098* stop_gained 0.12
rpoC 764669 p.Pro434Thr missense_variant 0.33
rpoC 765262 c.1893C>A synonymous_variant 0.12
rpoC 765421 c.2052C>A synonymous_variant 0.12
rpoC 766216 c.2847T>C synonymous_variant 0.15
rpoC 766467 p.Glu1033Ala missense_variant 0.36
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775755 p.Thr909Asn missense_variant 0.22
mmpL5 775952 c.2529G>A synonymous_variant 0.22
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776749 p.Phe578Leu missense_variant 0.2
mmpR5 778220 c.-770G>A upstream_gene_variant 0.13
mmpL5 778938 c.-459delC upstream_gene_variant 0.12
mmpR5 778996 p.Val3Phe missense_variant 0.14
mmpL5 779211 c.-731C>A upstream_gene_variant 0.12
rpsL 781372 c.-188T>G upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1305020 p.Ala697Asp missense_variant 0.13
Rv1258c 1406135 p.Glu402Asp missense_variant 0.13
Rv1258c 1406917 p.Ile142Val missense_variant 0.11
embR 1416970 c.378C>T synonymous_variant 0.13
embR 1417001 p.Val116Gly missense_variant 0.15
embR 1417399 c.-52G>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674152 p.Pro238Arg missense_variant 0.5
inhA 1674497 p.Pro99Gln missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101725 p.Thr440Ala missense_variant 0.11
ndh 2101967 p.Arg359Leu missense_variant 0.11
ndh 2102205 p.Val280Phe missense_variant 0.22
ndh 2102267 p.Val259Ala missense_variant 0.18
ndh 2103225 c.-183A>C upstream_gene_variant 0.43
katG 2154008 p.Ser702Pro missense_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155278 c.834C>A synonymous_variant 0.2
katG 2155529 p.Glu195* stop_gained 0.12
katG 2156256 c.-145C>A upstream_gene_variant 0.14
katG 2156499 c.-388C>A upstream_gene_variant 0.15
katG 2156543 c.-432G>A upstream_gene_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168437 p.Leu726Ile missense_variant 0.11
PPE35 2168485 p.Asn710Asp missense_variant 0.11
PPE35 2169138 p.Thr492Met missense_variant 0.2
PPE35 2169574 p.Phe347Leu missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.15
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2221838 p.Gly443Cys missense_variant 0.12
Rv1979c 2222951 p.Val72Ile missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288879 c.363G>T synonymous_variant 0.18
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518251 p.Leu46Pro missense_variant 0.12
eis 2714255 p.Tyr360His missense_variant 0.25
eis 2714807 p.Glu176* stop_gained 0.14
eis 2715303 p.Glu10Asp missense_variant 0.13
eis 2715328 p.Thr2Asn missense_variant 0.14
eis 2715363 c.-31G>C upstream_gene_variant 0.17
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.2
folC 2746873 p.Met242Ile missense_variant 0.14
folC 2746981 c.618T>C synonymous_variant 0.13
folC 2747353 c.246C>T synonymous_variant 0.12
folC 2747447 p.Ser51Ile missense_variant 0.18
folC 2747652 c.-54G>T upstream_gene_variant 0.15
folC 2747777 c.-179C>T upstream_gene_variant 0.2
pepQ 2859349 p.Gln357Arg missense_variant 0.18
ribD 2986925 c.87C>A synonymous_variant 0.11
ribD 2987414 c.576C>T synonymous_variant 0.11
Rv2752c 3065265 c.927C>G synonymous_variant 0.17
Rv2752c 3065555 c.636dupG frameshift_variant 0.17
thyX 3067720 p.Ala76Ser missense_variant 0.15
thyA 3074306 p.Ala56Ser missense_variant 0.19
thyA 3074574 c.-103G>A upstream_gene_variant 0.17
thyA 3074645 c.-174T>G upstream_gene_variant 0.27
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087228 p.Ala137Ser missense_variant 0.17
Rv3083 3448883 p.Glu127Val missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474102 c.96C>T synonymous_variant 0.2
fprA 3474393 c.387C>A synonymous_variant 0.17
fprA 3475075 p.Val357Ile missense_variant 0.15
Rv3236c 3613243 c.-127C>A upstream_gene_variant 0.12
fbiA 3640381 c.-162T>C upstream_gene_variant 0.62
fbiB 3640863 c.-672C>T upstream_gene_variant 0.33
fbiB 3642023 c.489C>G synonymous_variant 0.18
fbiB 3642185 c.651G>T synonymous_variant 0.2
fbiB 3642768 p.Leu412Met missense_variant 0.13
rpoA 3877839 c.669G>C synonymous_variant 0.17
rpoA 3878074 p.Gly145Ala missense_variant 0.4
rpoA 3878079 c.429C>A synonymous_variant 0.5
ddn 3986960 c.117C>G synonymous_variant 0.1
clpC1 4038186 p.Ala840Glu missense_variant 0.4
clpC1 4039142 p.Gln521His missense_variant 0.11
clpC1 4039535 c.1170C>A synonymous_variant 0.13
clpC1 4040556 p.Glu50Gly missense_variant 0.1
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240449 p.Gln196Arg missense_variant 0.12
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242461 p.Gly867Cys missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243323 p.Val31Ile missense_variant 0.88
embA 4244525 c.1293G>A synonymous_variant 0.17
embA 4244999 c.1767G>T synonymous_variant 0.22
embB 4246049 c.-465G>T upstream_gene_variant 0.12
embB 4246578 p.Ser22Phe missense_variant 0.18
embB 4247065 p.Gln184His missense_variant 0.12
embB 4247113 c.600G>C synonymous_variant 0.15
embB 4247865 p.Ala451Glu missense_variant 0.13
embB 4247876 p.Leu455Met missense_variant 0.12
embB 4248553 c.2040C>T synonymous_variant 0.14
embB 4249095 p.Ala861Glu missense_variant 0.18
embB 4249648 c.3135G>A synonymous_variant 0.17
aftB 4267195 p.Pro548Thr missense_variant 0.12
aftB 4268150 p.Met229Ile missense_variant 0.17
ethA 4326154 c.1320G>T synonymous_variant 0.14
ethA 4326376 c.1098G>T synonymous_variant 0.14
ethR 4326679 c.-870C>A upstream_gene_variant 0.17
ethA 4327002 p.Val158Ile missense_variant 0.22
ethA 4327344 p.Thr44Ala missense_variant 0.14
ethR 4327902 p.Lys118Asn missense_variant 0.12
ethA 4328377 c.-904C>A upstream_gene_variant 0.12
whiB6 4338239 p.Leu95Met missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407831 c.372G>T synonymous_variant 0.15
gid 4408242 c.-40T>C upstream_gene_variant 0.1