TB-Profiler result

Run: SRR3732580

Summary

Run ID: SRR3732580

Sample name:

Date: 04-04-2023 05:36:06

Number of reads: 2211807

Percentage reads mapped: 99.68

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 760314 p.Val170Phe missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289090 p.His51Arg missense_variant 1.0 pyrazinamide
embB 4249512 p.Met1000Arg missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.97
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766860 p.Arg1164Leu missense_variant 0.15
rpoC 767019 p.Thr1217Ile missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778100 p.Gln127His missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303424 p.Arg165Leu missense_variant 0.15
embR 1417173 p.Leu59Ile missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472865 n.1020C>A non_coding_transcript_exon_variant 0.18
rrs 1473295 n.1450G>T non_coding_transcript_exon_variant 0.12
rrl 1473991 n.334C>A non_coding_transcript_exon_variant 0.15
rrl 1474372 n.715C>A non_coding_transcript_exon_variant 0.22
rrl 1474782 n.1125G>T non_coding_transcript_exon_variant 0.22
rrl 1474975 n.1318G>T non_coding_transcript_exon_variant 0.17
rrl 1475640 n.1983G>T non_coding_transcript_exon_variant 0.22
rrl 1475766 n.2109G>T non_coding_transcript_exon_variant 0.13
rrl 1475962 n.2305G>A non_coding_transcript_exon_variant 0.17
rrl 1476189 n.2532C>A non_coding_transcript_exon_variant 0.14
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.17
inhA 1674498 c.297G>A synonymous_variant 0.15
rpsA 1834683 p.Ala381Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169782 c.831G>A synonymous_variant 0.15
PPE35 2169939 p.Gly225Ala missense_variant 0.12
PPE35 2169941 c.672C>T synonymous_variant 0.12
PPE35 2169944 c.669G>C synonymous_variant 0.13
PPE35 2169947 c.666T>C synonymous_variant 0.11
PPE35 2169983 c.630C>G synonymous_variant 0.1
PPE35 2170143 p.Gly157Val missense_variant 0.25
PPE35 2170146 p.Ser156Tyr missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289148 p.Ser32Gly missense_variant 0.12
pncA 2289258 c.-17G>T upstream_gene_variant 0.16
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746251 p.Ala450Ser missense_variant 0.12
pepQ 2859710 p.Phe237Leu missense_variant 0.13
Rv2752c 3064755 c.1437C>A synonymous_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339361 p.Asp82Asn missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612033 p.Met362Val missense_variant 0.11
ddn 3986911 p.Arg23Leu missense_variant 0.15
ddn 3986963 c.120C>A synonymous_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242374 c.-859C>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244373 p.Pro381Thr missense_variant 0.12
embB 4249760 p.Ala1083Ser missense_variant 0.14
ubiA 4268930 p.Gly302Cys missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407768 p.Leu145Phe missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0