TB-Profiler result

Run: SRR3732699
Summary

Run ID: SRR3732699

Sample name:

Date: 04-04-2023 05:37:59

Number of reads: 471723

Percentage reads mapped: 99.53

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 761161 p.Leu452Pro missense_variant 0.89 rifampicin
katG 2155168 p.Ser315Thr 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 5192 c.-48C>A upstream_gene_variant 0.14
gyrB 5272 c.33A>G synonymous_variant 0.15
gyrB 6262 p.Lys341Asn missense_variant 0.12
gyrA 6751 c.-551G>A upstream_gene_variant 0.33
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
fgd1 490713 c.-70G>T upstream_gene_variant 0.12
fgd1 491571 p.Asp263Glu missense_variant 0.4
mshA 575588 p.Arg81Ser missense_variant 0.29
mshA 575591 c.248dupG frameshift_variant 0.29
mshA 576275 p.Asp310Tyr missense_variant 0.33
mshA 576567 p.Arg407Leu missense_variant 0.33
rpoC 763612 p.Glu81Asp missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765812 c.2443C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776549 c.1932C>A synonymous_variant 0.25
mmpS5 778495 p.Cys137* stop_gained 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801414 c.606C>A synonymous_variant 0.17
fbiC 1302811 c.-120G>T upstream_gene_variant 0.2
fbiC 1302814 c.-117C>A upstream_gene_variant 0.2
fbiC 1303687 c.759delT frameshift_variant 0.33
embR 1417200 p.Val50Leu missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473601 n.-57C>A upstream_gene_variant 0.33
rrl 1474239 n.582G>T non_coding_transcript_exon_variant 0.5
fabG1 1673339 c.-101C>A upstream_gene_variant 0.18
fabG1 1673560 p.Lys41Leu missense_variant 0.2
tlyA 1917926 c.-14G>T upstream_gene_variant 0.67
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102041 p.Gln334His missense_variant 0.2
katG 2156221 c.-110C>T upstream_gene_variant 0.14
PPE35 2167727 c.2886C>A synonymous_variant 0.22
Rv1979c 2221739 p.Asp476Tyr missense_variant 0.25
Rv1979c 2222827 p.Phe113Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288687 p.Ser185Arg missense_variant 0.29
kasA 2518516 c.402C>A synonymous_variant 0.13
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747370 p.Ser77Pro missense_variant 0.13
folC 2747389 c.210G>T synonymous_variant 0.13
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087529 p.Gly237Val missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612277 c.840G>A synonymous_variant 0.29
fbiA 3640685 p.Gly48Val missense_variant 0.4
fbiB 3642123 p.Glu197* stop_gained 0.29
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038651 p.Gly685Val missense_variant 0.25
clpC1 4040540 c.165G>A synonymous_variant 0.14
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245311 c.2079C>A synonymous_variant 0.17
embB 4247045 p.Asp178Tyr missense_variant 0.4
embB 4248075 p.Glu521Ala missense_variant 0.22
ethR 4326721 c.-828G>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0