TB-Profiler result

Run: SRR12199422
Summary

Run ID: SRR12199422

Sample name:

Date: 03-04-2023 06:38:48

Number of reads: 422792

Percentage reads mapped: 38.48

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 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
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
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 9573 p.Arg758Trp missense_variant 0.15
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
ccsA 620837 p.Gly316Asp missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765546 p.Arg726His missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776109 p.Met791Arg missense_variant 0.25
mmpL5 776124 p.Leu786Pro missense_variant 0.25
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776367 p.Leu705Pro missense_variant 0.12
mmpL5 776942 c.1539A>G synonymous_variant 0.15
mmpS5 778482 p.Ala142Ser missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800943 c.137delG frameshift_variant 0.11
fbiC 1303064 p.Ala45Val missense_variant 0.14
fbiC 1305347 p.Asp806Val missense_variant 0.11
Rv1258c 1406598 p.Pro248Arg missense_variant 0.1
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1460891 c.-153delA upstream_gene_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475195 n.1538G>T non_coding_transcript_exon_variant 0.22
fabG1 1673346 c.-94C>G upstream_gene_variant 0.1
fabG1 1673349 c.-91G>C upstream_gene_variant 0.1
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834201 c.660C>G synonymous_variant 0.14
rpsA 1834683 p.Ala381Val missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918092 c.153G>A synonymous_variant 0.33
ndh 2102305 c.738T>C synonymous_variant 0.22
katG 2154693 c.1419T>C synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156038 p.His25Arg missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169094 p.Thr507Ser missense_variant 0.12
PPE35 2169488 c.1125G>C synonymous_variant 0.18
PPE35 2169491 c.1122T>C synonymous_variant 0.18
PPE35 2169578 c.1035T>C synonymous_variant 0.11
PPE35 2169598 p.Phe339Ile missense_variant 0.12
PPE35 2169606 p.Asn336Thr missense_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2169910 p.Asn235Tyr missense_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.7
PPE35 2170053 p.Thr187Ser missense_variant 0.7
Rv1979c 2222842 c.322delG frameshift_variant 0.2
Rv1979c 2223010 p.Val52Gly missense_variant 1.0
Rv1979c 2223157 p.Gly3Asp missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289327 c.-86C>T upstream_gene_variant 0.15
pncA 2289497 c.-256G>C upstream_gene_variant 0.18
kasA 2518423 c.309C>A synonymous_variant 0.12
kasA 2519140 c.1026G>C synonymous_variant 0.17
kasA 2519143 c.1029G>C synonymous_variant 0.13
eis 2714934 c.399C>T synonymous_variant 0.14
ahpC 2726169 c.-24T>C upstream_gene_variant 0.11
ribD 2986878 p.Leu14Val missense_variant 0.1
Rv2752c 3064564 p.Glu543Gly missense_variant 0.33
Rv2752c 3065080 p.His371Arg missense_variant 0.12
Rv2752c 3066157 p.Thr12Ile missense_variant 0.25
thyA 3074645 c.-174T>G upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612728 p.Ser130Leu missense_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640831 p.Val97Met missense_variant 0.13
alr 3840991 p.Ala144Thr missense_variant 0.12
clpC1 4038948 p.His586Arg missense_variant 0.15
clpC1 4040144 c.561G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244902 p.Ala557Val missense_variant 0.13
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246567 c.54G>T synonymous_variant 0.29
aftB 4267154 c.1683A>G synonymous_variant 0.1
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268521 p.Tyr106Asn missense_variant 0.18
ethR 4326883 c.-666C>T upstream_gene_variant 0.2
whiB6 4338510 c.12T>C synonymous_variant 1.0
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