TB-Profiler result

Run: SRR11972223
Summary

Run ID: SRR11972223

Sample name:

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

Number of reads: 466113

Percentage reads mapped: 98.97

Strain: lineage2.2.1.1

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
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 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
inhA 1674248 p.Ile16Thr missense_variant 0.18 isoniazid
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 5119 c.-121T>A upstream_gene_variant 0.17
gyrB 6136 c.897G>A synonymous_variant 0.12
gyrB 6810 p.Tyr524Phe missense_variant 0.14
gyrB 7170 p.Ala644Asp missense_variant 0.13
gyrA 7186 c.-116C>T upstream_gene_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9406 p.Gly702Val missense_variant 0.18
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 759939 p.Pro45Thr missense_variant 1.0
rpoB 761378 c.1572C>T synonymous_variant 1.0
rpoB 761579 c.1773G>A synonymous_variant 0.13
rpoB 762652 p.Trp949* stop_gained 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764459 p.Glu364* stop_gained 0.12
rpoC 766248 p.Val960Ala missense_variant 0.12
rpoC 766315 c.2946C>A synonymous_variant 0.15
rpoC 766996 c.3627C>A synonymous_variant 0.18
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 777433 p.Ala350Thr missense_variant 0.17
mmpL5 778086 c.394delG frameshift_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781411 c.-149G>T upstream_gene_variant 0.15
fbiC 1303486 p.Gly186Arg missense_variant 0.15
fbiC 1304354 p.Ser475Leu missense_variant 0.13
Rv1258c 1406227 p.Asp372Asn missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461236 p.Tyr64* stop_gained 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472249 n.404T>G non_coding_transcript_exon_variant 0.11
rrs 1472549 n.704G>A non_coding_transcript_exon_variant 0.17
rrs 1472951 n.1106T>C non_coding_transcript_exon_variant 0.15
rrs 1472953 n.1108G>A non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.18
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.11
rrl 1473461 n.-197T>C upstream_gene_variant 0.15
rrl 1474553 n.896T>C non_coding_transcript_exon_variant 1.0
rrl 1474980 n.1323G>T non_coding_transcript_exon_variant 0.13
rrl 1475156 n.1499G>T non_coding_transcript_exon_variant 0.11
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.11
inhA 1674138 c.-64C>T upstream_gene_variant 0.12
inhA 1674759 c.558G>A synonymous_variant 0.4
rpsA 1833504 c.-38T>C upstream_gene_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918217 p.Thr93Ile missense_variant 0.15
ndh 2101988 p.Ala352Val missense_variant 0.18
ndh 2102133 p.Gln304Lys missense_variant 0.12
ndh 2102914 c.129C>T synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155280 p.Ala278Thr missense_variant 0.18
katG 2155431 c.681G>A synonymous_variant 0.18
PPE35 2167821 p.Ser931* stop_gained 0.14
PPE35 2167833 p.Leu927Arg missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167930 p.Ser895Pro missense_variant 0.17
PPE35 2169238 p.Asp459Asn missense_variant 0.17
PPE35 2169464 c.1149C>T synonymous_variant 0.14
PPE35 2169534 p.Gly360Val missense_variant 0.12
PPE35 2169542 c.1071C>T synonymous_variant 0.12
Rv1979c 2222660 p.Gly169Cys missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289385 c.-144C>T upstream_gene_variant 0.17
eis 2714846 p.Val163Ile missense_variant 1.0
folC 2746145 p.Asp485Gly missense_variant 0.18
folC 2746249 c.1350C>T synonymous_variant 0.12
Rv2752c 3065184 c.1008G>A synonymous_variant 0.13
Rv2752c 3065357 p.Leu279Val missense_variant 0.18
Rv2752c 3066303 c.-112C>A upstream_gene_variant 0.15
thyA 3074034 c.438T>C synonymous_variant 0.18
thyA 3074496 c.-25C>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339376 p.Asp87Tyr missense_variant 0.2
Rv3083 3448305 c.-199T>C upstream_gene_variant 0.12
Rv3083 3448512 p.Gln3His missense_variant 0.13
Rv3083 3449052 c.549C>T synonymous_variant 0.18
Rv3083 3449290 p.Lys263* stop_gained 0.15
Rv3083 3449987 p.Ala495Gly missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474143 p.Trp46Tyr missense_variant 0.25
Rv3236c 3612699 p.Leu140Met missense_variant 0.17
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3642540 p.Ala336Thr missense_variant 0.15
alr 3840648 p.Tyr258Cys missense_variant 0.12
alr 3841067 c.354C>A synonymous_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.26
rpoA 3877505 p.Ala335Ser missense_variant 0.15
rpoA 3877598 c.910C>T synonymous_variant 0.17
rpoA 3878090 p.Val140Ile missense_variant 0.2
ddn 3986860 p.Pro6Leu missense_variant 0.13
clpC1 4038502 p.Ile735Phe missense_variant 0.15
clpC1 4039509 p.Ala399Val missense_variant 0.22
clpC1 4039645 p.His354Asp missense_variant 0.13
clpC1 4039738 p.Thr323Ala missense_variant 0.12
clpC1 4040416 p.Gln97Lys missense_variant 0.11
clpC1 4040638 p.Leu23Val missense_variant 0.12
panD 4043870 p.Val138Leu missense_variant 0.12
panD 4044271 p.Thr4Met missense_variant 0.11
embC 4240475 p.Ala205Thr missense_variant 0.13
embC 4241174 p.Ser438Pro missense_variant 0.14
embC 4241905 c.2043C>T synonymous_variant 0.13
embC 4242207 p.Ser782Phe missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4246059 p.Ala943Ser missense_variant 0.2
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.21
embB 4246555 c.42G>C synonymous_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.2
embB 4247867 p.Val452Met missense_variant 0.12
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249062 p.Thr850Ile missense_variant 0.12
aftB 4267285 p.Thr518Ala missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327137 p.Glu113Lys missense_variant 0.2
whiB6 4338250 p.Ala91Glu missense_variant 0.14
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