TB-Profiler result

Run: SRR11972211
Summary

Run ID: SRR11972211

Sample name:

Date: 03-04-2023 05:32:12

Number of reads: 258497

Percentage reads mapped: 99.35

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288956 p.Lys96Glu missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327148 p.Trp109* stop_gained 1.0 ethionamide
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 6843 p.Val535Asp missense_variant 0.15
gyrB 7158 c.1931_1933delCCG disruptive_inframe_deletion 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8270 c.969G>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761030 c.1224G>C synonymous_variant 0.13
rpoB 761510 c.1704T>C synonymous_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Ala missense_variant 0.86
rpoC 765707 p.Glu780Lys missense_variant 0.13
mmpL5 775612 p.Ser957Thr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 779434 p.Val149Phe missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833766 p.Asp75Glu missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154952 p.Asp387Gly missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170337 c.276G>T synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288880 p.Arg121Gln missense_variant 0.2
pncA 2288896 c.346C>T synonymous_variant 0.2
pepQ 2860278 c.141C>A synonymous_variant 0.14
ribD 2987160 p.Ala108Thr missense_variant 0.29
Rv2752c 3064775 c.1416delT frameshift_variant 1.0
thyX 3067727 c.219A>C synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338927 c.-191C>T upstream_gene_variant 0.11
fbiD 3339102 c.-16C>T upstream_gene_variant 0.2
Rv3083 3449745 c.1242C>T synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474687 c.681G>C synonymous_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613279 c.-163C>T upstream_gene_variant 0.22
fbiB 3641606 c.72T>G synonymous_variant 0.18
alr 3840720 p.Leu234Pro missense_variant 0.13
clpC1 4038888 p.Glu606Val missense_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244743 p.Phe504Tyr missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268446 p.Ala131Thr missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0