TB-Profiler result

Run: SRR11972442

Summary

Run ID: SRR11972442

Sample name:

Date: 03-04-2023 05:42:32

Number of reads: 810095

Percentage reads mapped: 94.34

Strain: lineage1.1.3

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
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 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
folC 2747141 p.Glu153Ala missense_variant 0.97 para-aminosalicylic_acid
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 5436 p.Asn66Ser missense_variant 1.0
gyrB 6084 p.Gly282Val missense_variant 1.0
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7926 p.Asp209Asn missense_variant 0.12
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491334 c.552C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.31
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303016 p.Val29Gly missense_variant 0.24
Rv1258c 1407358 c.-18G>A upstream_gene_variant 0.13
embR 1417019 p.Cys110Tyr missense_variant 0.95
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472753 n.908A>C non_coding_transcript_exon_variant 1.0
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.13
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
eis 2715355 c.-23G>A upstream_gene_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.91
ahpC 2726338 p.Val49Gly missense_variant 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065540 p.Val218Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474268 p.Val88Ile missense_variant 0.17
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
alr 3840391 p.Asp344Asn missense_variant 1.0
clpC1 4038169 c.2531_2535delAGCCG frameshift_variant 0.15
clpC1 4038178 c.2526_2527insT frameshift_variant 0.13
clpC1 4038183 p.Gly841Ala missense_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242432 p.Gly857Asp missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249602 p.Asp1030Gly missense_variant 1.0
aftB 4267814 c.1023G>A synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4328412 c.-939G>A upstream_gene_variant 1.0
whiB6 4338243 c.278delG frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 1.0
gid 4407861 p.Ile114Arg missense_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0