TB-Profiler result

Run: SRR4033458
Summary

Run ID: SRR4033458

Sample name:

Date: 04-04-2023 06:06:38

Number of reads: 978208

Percentage reads mapped: 99.68

Strain: 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 0.98
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.2 Euro-American (LAM) LAM3 None 1.0
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
pncA 2289006 p.Ala79Gly missense_variant 0.12 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.12 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 5520 p.Pro94Leu missense_variant 1.0
gyrB 5828 p.Met197Leu missense_variant 0.25
gyrB 6164 p.Asn309Tyr missense_variant 0.14
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7507 p.Ser69Ile missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9070 p.Thr590Met missense_variant 0.2
gyrA 9109 p.Gln603Arg missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491159 p.Lys126Met missense_variant 0.14
fgd1 491357 p.Phe192Ser missense_variant 0.18
fgd1 491422 p.Gly214Cys missense_variant 0.13
mshA 576752 p.Pro469Ser missense_variant 0.15
mshA 576757 c.1410C>T synonymous_variant 0.14
mshA 576770 p.Arg475Cys missense_variant 0.13
ccsA 619724 c.-167C>T upstream_gene_variant 0.14
rpoB 759711 c.-96G>C upstream_gene_variant 0.12
rpoB 760552 p.Ser249Phe missense_variant 0.15
rpoB 760577 c.773dupA frameshift_variant 0.17
rpoB 760807 p.Ala334Val missense_variant 0.17
rpoB 760966 p.Met387Lys missense_variant 0.18
rpoB 760979 p.Glu391Asp missense_variant 0.17
rpoB 761596 p.Asn597Ser missense_variant 0.13
rpoB 761699 p.Asp631Glu missense_variant 0.12
rpoC 763865 p.Arg166Cys missense_variant 0.13
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765715 c.2346C>T synonymous_variant 0.2
rpoC 766905 p.Ser1179Leu missense_variant 0.13
rpoC 767183 p.Val1272Leu missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776160 p.Tyr774Cys missense_variant 0.13
mmpL5 776696 c.1784delC frameshift_variant 0.14
mmpL5 776877 p.Gln535Leu missense_variant 0.22
mmpL5 776897 c.1584C>T synonymous_variant 0.22
mmpL5 777164 c.1317C>G synonymous_variant 0.5
mmpL5 777167 c.1313delT frameshift_variant 0.5
mmpL5 777304 p.Ile393Phe missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407248 c.93G>A synonymous_variant 0.14
embR 1417307 p.Gly14Asp missense_variant 0.18
embR 1417318 c.30G>A synonymous_variant 0.13
embR 1417448 c.-101G>C upstream_gene_variant 0.12
atpE 1461059 c.15C>T synonymous_variant 0.18
rrs 1471656 n.-190G>A upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473491 n.-167C>A upstream_gene_variant 0.15
rrl 1476155 n.2498C>G non_coding_transcript_exon_variant 0.25
fabG1 1673343 c.-97A>G upstream_gene_variant 0.12
fabG1 1673362 c.-78C>A upstream_gene_variant 0.15
inhA 1674075 c.-127C>G upstream_gene_variant 0.22
rpsA 1833899 p.Lys120* stop_gained 0.18
rpsA 1834543 c.1002C>A synonymous_variant 0.22
rpsA 1834797 p.Ala419Gly missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102546 p.Arg166Leu missense_variant 0.18
katG 2153960 p.Pro718Ser missense_variant 0.18
katG 2153968 p.Asp715Gly missense_variant 0.18
katG 2154915 p.Glu399Asp missense_variant 0.13
katG 2154923 p.Trp397Arg missense_variant 0.15
katG 2155738 p.Gly125Asp missense_variant 0.13
PPE35 2167961 c.2652G>T synonymous_variant 0.22
PPE35 2170086 p.Ala176Glu missense_variant 0.22
PPE35 2170398 c.214delT frameshift_variant 0.25
PPE35 2170664 c.-52C>T upstream_gene_variant 0.12
Rv1979c 2222678 p.Asn163Tyr missense_variant 0.14
Rv1979c 2222817 c.347delC frameshift_variant 0.22
Rv1979c 2222933 p.Ser78Pro missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289871 c.-630T>A upstream_gene_variant 0.18
pncA 2290137 c.-896A>G upstream_gene_variant 0.14
eis 2714697 c.636T>C synonymous_variant 0.12
ahpC 2726079 c.-114G>C upstream_gene_variant 0.1
ribD 2986858 p.Leu7Pro missense_variant 0.11
ribD 2987030 c.195delC frameshift_variant 0.12
thyX 3067528 p.Arg140Cys missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449539 p.Thr346Ser missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474154 p.Arg50Ser missense_variant 0.13
fprA 3474162 c.156G>A synonymous_variant 0.12
fprA 3474167 p.Ala54Gly missense_variant 0.14
fprA 3474937 p.Glu311* stop_gained 0.15
fbiA 3640556 p.Val5Ala missense_variant 0.11
alr 3841098 p.Pro108Gln missense_variant 0.17
alr 3841390 p.Pro11Thr missense_variant 0.15
alr 3841602 c.-182C>A upstream_gene_variant 0.18
alr 3841615 c.-195T>C upstream_gene_variant 0.18
rpoA 3877494 p.Glu338Asp missense_variant 0.13
rpoA 3877670 p.Glu280* stop_gained 0.13
rpoA 3877684 p.Leu275Gln missense_variant 0.13
rpoA 3878155 p.Val118Glu missense_variant 0.14
rpoA 3878299 p.Lys70Arg missense_variant 0.11
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039616 c.1089G>T synonymous_variant 0.17
clpC1 4040510 c.194delA frameshift_variant 0.15
clpC1 4040904 c.-200G>A upstream_gene_variant 0.18
embC 4240083 p.Leu74Pro missense_variant 0.17
embC 4242574 p.Glu904Asp missense_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243738 p.Gln169Arg missense_variant 0.11
embA 4245159 p.Ser643Gly missense_variant 0.11
embB 4247107 c.594C>T synonymous_variant 0.17
embB 4247847 p.Gln445Arg missense_variant 0.13
aftB 4268239 p.Met200Val missense_variant 0.12
ubiA 4269803 p.Ala11Thr missense_variant 0.17
ethA 4326486 p.Gly330Ser missense_variant 0.18
ethA 4326615 p.Asn287Asp missense_variant 0.12
ethA 4328434 c.-961C>A upstream_gene_variant 0.15
whiB6 4338365 p.Cys53Arg missense_variant 0.11
whiB6 4338399 p.Trp41* stop_gained 0.15
whiB6 4338422 p.Cys34Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407604 p.Ala200Gly missense_variant 0.12
gid 4408156 p.Leu16Arg missense_variant 1.0