TB-Profiler result

Run: SRR11972262
Summary

Run ID: SRR11972262

Sample name:

Date: 03-04-2023 05:34:07

Number of reads: 420865

Percentage reads mapped: 99.55

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 0.99
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 2289207 p.Asp12Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile 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
gyrB 6007 c.768C>T synonymous_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8433 p.Thr378Ala missense_variant 0.11
gyrA 8944 p.Gly548Ala missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491339 p.Gly186Asp missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575940 p.Leu198Arg missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759810 p.Ala2Ser missense_variant 0.13
rpoB 760514 c.709delT frameshift_variant 0.12
rpoB 760525 p.Glu240Ala missense_variant 0.12
rpoB 760927 p.Thr374Met missense_variant 0.14
rpoB 761773 p.His656Pro missense_variant 1.0
rpoC 762770 c.-600C>T upstream_gene_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763424 p.Asp19His missense_variant 0.29
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765114 p.Val582Ala missense_variant 0.11
rpoC 765931 c.2562C>T synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776492 c.1989G>A synonymous_variant 0.13
mmpL5 776725 p.Tyr586His missense_variant 0.11
mmpR5 778082 c.-908T>C upstream_gene_variant 0.12
mmpS5 778845 p.Ala21Thr missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303652 p.Arg241Gln missense_variant 0.18
fbiC 1304483 p.Ala518Val missense_variant 0.12
fbiC 1304487 c.1557C>A synonymous_variant 0.12
fbiC 1304977 p.Gly683Ser missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416533 p.Gly272Val missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673611 p.Val58Ile missense_variant 0.22
inhA 1674367 p.Ala56Thr missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834407 p.Arg289His missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154081 c.2031C>G synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155697 p.Ala139Thr missense_variant 0.17
katG 2156521 c.-410C>T upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170298 c.315A>G synonymous_variant 0.11
PPE35 2170308 p.Leu102Ala missense_variant 0.11
PPE35 2170313 c.300G>C synonymous_variant 0.11
Rv1979c 2221972 p.Arg398Lys missense_variant 0.12
Rv1979c 2222109 c.1056C>T synonymous_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714522 p.Pro271Ser missense_variant 0.13
ahpC 2726650 p.Ser153Leu missense_variant 0.12
ribD 2987146 p.Arg103Leu missense_variant 0.22
ribD 2987188 p.Leu117Pro missense_variant 0.25
ribD 2987553 p.Arg239Cys missense_variant 0.15
Rv2752c 3065810 p.Val128Ile missense_variant 0.13
Rv2752c 3065996 p.His66Asp missense_variant 0.11
thyA 3074380 p.Gly31Asp missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339336 c.219C>T synonymous_variant 0.12
fbiD 3339415 p.Glu100Lys missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474331 p.Asp109Asn missense_variant 0.22
fprA 3474515 p.Pro170His missense_variant 0.33
fprA 3474716 p.Asp237Gly missense_variant 0.33
Rv3236c 3612735 p.Ser128Thr missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642288 p.Gly252Ser missense_variant 0.17
alr 3840309 c.1111delC frameshift_variant 0.12
alr 3840938 c.483G>A synonymous_variant 0.12
rpoA 3877655 p.Asp285Asn missense_variant 0.12
clpC1 4040103 p.Met201Thr missense_variant 0.1
embC 4241032 c.1170G>A synonymous_variant 0.13
embC 4241039 p.Asp393Asn missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244352 p.Pro374Ser missense_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.14
embB 4246555 c.42G>C synonymous_variant 0.14
embB 4246556 p.Ala15Pro missense_variant 0.14
embB 4247717 p.Leu402Val missense_variant 1.0
embB 4247794 c.1281G>A synonymous_variant 0.14
aftB 4266993 p.Leu615Pro missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268221 p.Thr206Ser missense_variant 0.12
ubiA 4269238 p.Ala199Gly missense_variant 0.17
ethA 4326666 p.Arg270Cys missense_variant 0.12
ethR 4326940 c.-609G>A upstream_gene_variant 0.12
ethR 4327447 c.-102G>A upstream_gene_variant 0.15
whiB6 4338327 c.195C>T synonymous_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.92
gid 4407927 p.Glu92Asp missense_variant 1.0