TB-Profiler result

Run: SRR12199433

Summary

Run ID: SRR12199433

Sample name:

Date: 03-04-2023 06:39:21

Number of reads: 144528

Percentage reads mapped: 92.88

Strain: lineage4;lineage1.1

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 0.9
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.08
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
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
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 1.0
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 760490 c.684C>T synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765171 p.Pro601Leu missense_variant 1.0
mmpL5 776395 p.Phe696Leu missense_variant 1.0
mmpL5 776745 p.Arg579Pro missense_variant 0.67
mmpL5 778926 c.-446A>G upstream_gene_variant 0.4
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473491 n.-167C>A upstream_gene_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102129 p.Val305Glu missense_variant 0.29
ndh 2102209 c.834C>A synonymous_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167955 c.2658A>C synonymous_variant 0.5
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169807 p.Leu269Pro missense_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.83
PPE35 2170053 p.Thr187Ser missense_variant 0.83
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
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087604 p.Ala262Val missense_variant 0.5
fbiD 3339273 c.156T>G synonymous_variant 0.33
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
Rv3236c 3612994 p.Leu41Phe missense_variant 0.5
alr 3841539 c.-119C>T upstream_gene_variant 0.29
alr 3841546 c.-126C>A upstream_gene_variant 0.38
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embB 4248814 c.2301G>A synonymous_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269777 c.-941G>A upstream_gene_variant 0.67
ethA 4328200 c.-727C>A upstream_gene_variant 0.17
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 4407873 c.330G>T synonymous_variant 1.0