TB-Profiler result

Run: ERR176616

Summary

Run ID: ERR176616

Sample name:

Date: 31-03-2023 15:07:33

Number of reads: 2805483

Percentage reads mapped: 99.6

Strain: lineage4.3.4.2.1;lineage1.1.3.2

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 0.65
lineage1 Indo-Oceanic EAI RD239 0.37
lineage4.3 Euro-American (LAM) mainly-LAM None 0.61
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.34
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.39
lineage4.3.4 Euro-American (LAM) LAM RD174 0.63
lineage1.1.3.2 Indo-Oceanic NA RD239 0.35
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.64
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.6
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 0.58 rifampicin
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 0.76 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.69 isoniazid
pncA 2288820 p.Gln141Pro missense_variant 0.66 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.62 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 6112 p.Met291Ile missense_variant 0.45
gyrB 6140 p.Val301Leu missense_variant 0.56
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 0.37
gyrA 8452 p.Ala384Val missense_variant 0.43
gyrA 9143 c.1842T>C synonymous_variant 0.39
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.39
ccsA 619695 c.-196G>A upstream_gene_variant 0.45
rpoB 762714 p.Val970Met missense_variant 0.64
rpoC 763031 c.-339T>C upstream_gene_variant 0.27
rpoC 763884 p.Ala172Val missense_variant 0.38
rpoC 763886 c.517C>A synonymous_variant 0.4
rpoC 764995 c.1626C>G synonymous_variant 0.62
rpoC 765171 p.Pro601Leu missense_variant 0.34
rpoC 765230 p.Ala621Thr missense_variant 0.37
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.31
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 0.43
embR 1417019 p.Cys110Tyr missense_variant 0.3
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674883 p.Ile228Val missense_variant 0.36
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102540 p.Ala168Gly missense_variant 0.3
katG 2154724 p.Arg463Leu missense_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 0.35
PPE35 2167983 p.Gly877Asp missense_variant 0.32
PPE35 2169320 p.Leu431Phe missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 0.35
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.39
ahpC 2726051 c.-142G>A upstream_gene_variant 0.3
ahpC 2726338 p.Val49Gly missense_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 0.35
thyA 3073868 p.Thr202Ala missense_variant 0.67
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.39
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.33
fprA 3475159 p.Asn385Asp missense_variant 0.46
Rv3236c 3612009 p.Ala370Thr missense_variant 0.54
fbiB 3642173 c.639G>A synonymous_variant 0.36
alr 3840719 c.702A>G synonymous_variant 0.67
rpoA 3878687 c.-180A>C upstream_gene_variant 0.31
clpC1 4038287 c.2418C>T synonymous_variant 0.64
clpC1 4040517 p.Val63Ala missense_variant 0.42
embC 4240671 p.Thr270Ile missense_variant 0.39
embC 4241042 p.Asn394Asp missense_variant 0.4
embC 4241539 c.1677T>C synonymous_variant 0.56
embC 4242425 p.Arg855Gly missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.46
embA 4245969 p.Pro913Ser missense_variant 0.34
embB 4247646 p.Glu378Ala missense_variant 0.48
embB 4248730 c.2217C>T synonymous_variant 0.46
ubiA 4269387 p.Glu149Asp missense_variant 0.35
aftB 4269606 c.-770T>C upstream_gene_variant 0.4
ethA 4327229 p.Leu82Pro missense_variant 0.64
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.4
gid 4407588 c.615A>G synonymous_variant 0.34
gid 4407780 c.423G>A synonymous_variant 0.25
gid 4407873 c.330G>T synonymous_variant 0.32
gid 4408156 p.Leu16Arg missense_variant 0.54