TB-Profiler result

Run: ERR1194816

Summary

Run ID: ERR1194816

Sample name:

Date: 31-03-2023 12:34:38

Number of reads: 482107

Percentage reads mapped: 99.4

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.98
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
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 5847 p.Gly203Glu missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7374 p.Gln25Lys missense_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7639 p.Gln113Leu missense_variant 0.67
gyrA 8496 p.Asp399Asn missense_variant 0.22
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
mshA 576108 p.Ala254Gly missense_variant 0.5
mshA 576495 p.Asp383Gly missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760168 p.Met121Lys missense_variant 0.18
rpoB 760985 c.1179G>T synonymous_variant 0.29
rpoB 761197 p.Leu464Arg missense_variant 0.29
rpoB 762787 p.Val994Gly missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764543 p.Thr392Pro missense_variant 0.38
rpoC 764693 p.Gly442Ser missense_variant 0.12
rpoC 766520 p.Gly1051Ser missense_variant 0.33
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776092 p.Ser797Cys missense_variant 0.29
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776254 p.Lys743* stop_gained 0.33
mmpL5 776578 p.Thr635Pro missense_variant 0.23
mmpL5 776626 p.Asn619His missense_variant 0.18
mmpL5 777119 p.His454Gln missense_variant 0.13
mmpL5 777122 c.1359C>T synonymous_variant 0.13
mmpL5 777128 c.1353A>G synonymous_variant 0.13
mmpL5 778078 p.Thr135Pro missense_variant 0.18
mmpS5 779556 c.-651T>G upstream_gene_variant 0.27
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800750 c.-59G>A upstream_gene_variant 0.22
fbiC 1304430 c.1500A>C synonymous_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474326 n.669T>A non_coding_transcript_exon_variant 0.4
fabG1 1673253 c.-187A>T upstream_gene_variant 0.29
rpsA 1833560 p.Thr7Pro missense_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834320 p.Val260Gly missense_variant 0.38
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917976 p.Arg13Gly missense_variant 0.67
tlyA 1918084 p.Thr49Ala missense_variant 1.0
ndh 2102604 c.439T>C synonymous_variant 0.29
ndh 2102652 p.Phe131Ile missense_variant 0.29
ndh 2102892 p.Phe51Ile missense_variant 0.33
katG 2154332 p.Phe594Leu missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154992 p.Ser374Ala missense_variant 0.29
katG 2155251 p.Glu287Asp missense_variant 0.4
katG 2156044 p.Val23Glu missense_variant 0.18
katG 2156127 c.-16T>A upstream_gene_variant 0.2
katG 2156327 c.-216A>G upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168896 p.Gly573Cys missense_variant 0.2
PPE35 2169602 c.1011C>A synonymous_variant 0.2
PPE35 2169650 p.Leu321Phe missense_variant 0.18
PPE35 2169806 c.807T>A synonymous_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.23
PPE35 2170053 p.Thr187Ser missense_variant 0.23
PPE35 2170429 p.Ser62Ala missense_variant 0.29
PPE35 2170436 c.177T>G synonymous_variant 0.22
Rv1979c 2223155 p.Pro4Thr missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289301 c.-60T>A upstream_gene_variant 0.5
kasA 2518563 p.Ala150Asp missense_variant 0.4
eis 2715228 c.105C>A synonymous_variant 0.33
pepQ 2859332 p.Thr363Pro missense_variant 0.17
ribD 2986662 c.-177T>G upstream_gene_variant 0.22
ribD 2987301 p.Arg155Trp missense_variant 0.25
ribD 2987571 p.Thr245Ala missense_variant 0.29
Rv2752c 3065500 p.Gly231Val missense_variant 1.0
Rv2752c 3066022 p.Val57Gly missense_variant 0.3
Rv2752c 3067036 c.-845A>C upstream_gene_variant 0.67
Rv2752c 3067172 c.-981A>C upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339698 p.Asp194Ala missense_variant 0.3
Rv3083 3449035 p.Lys178* stop_gained 0.33
Rv3083 3449406 c.903C>A synonymous_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474507 c.501C>A synonymous_variant 0.25
fprA 3474669 c.663T>G synonymous_variant 0.33
fbiA 3641117 p.Lys192Met missense_variant 0.5
fbiB 3642757 p.Val408Gly missense_variant 0.5
fbiB 3642769 p.Leu412Arg missense_variant 0.67
alr 3840305 c.1116T>G synonymous_variant 0.22
alr 3840775 p.Thr216Pro missense_variant 0.25
rpoA 3878387 p.Thr41Pro missense_variant 0.22
embC 4240333 p.Phe157Leu missense_variant 0.2
embC 4241226 p.Pro455Gln missense_variant 0.2
embC 4241288 p.Ile476Leu missense_variant 0.25
embC 4241737 c.1875G>T synonymous_variant 0.2
embC 4241829 p.Lys656Arg missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242708 p.Asp949Ala missense_variant 0.43
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244054 c.822C>T synonymous_variant 0.2
embB 4246331 c.-183C>T upstream_gene_variant 0.4
embB 4247028 p.Leu172Gln missense_variant 0.5
embB 4247156 p.Thr215Pro missense_variant 0.33
embB 4247183 p.Gly224Arg missense_variant 0.33
embB 4248634 c.2121A>C synonymous_variant 0.25
aftB 4266957 p.Glu627Val missense_variant 0.29
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268031 p.Pro269Gln missense_variant 0.29
aftB 4268547 p.Leu97Arg missense_variant 0.22
aftB 4268619 p.Val73Gly missense_variant 0.5
whiB6 4338357 c.165T>C synonymous_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338676 c.-155T>G upstream_gene_variant 0.11
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0