TB-Profiler result

Run: ERR6336758
Summary

Run ID: ERR6336758

Sample name:

Date: 02-04-2023 02:02:10

Number of reads: 1237196

Percentage reads mapped: 99.29

Strain: lineage1.2.1.2.1

Drug-resistance: RR-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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1 Indo-Oceanic EAI2 RD239 1.0
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic NA RD239 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 761143 p.Lys446Thr missense_variant 0.18 rifampicin
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 5482 c.243C>A synonymous_variant 0.5
gyrB 5886 p.Asp216Gly missense_variant 0.15
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7819 p.Leu173Pro missense_variant 0.14
gyrA 7821 c.520C>T synonymous_variant 0.14
gyrA 7857 p.Ala186Thr missense_variant 0.14
gyrA 8354 c.1053G>C synonymous_variant 0.12
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9610 p.Asp770Val missense_variant 0.13
gyrA 9740 c.2439G>A synonymous_variant 0.95
fgd1 491335 p.Ala185Thr missense_variant 0.5
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575408 p.Gly21Ser missense_variant 0.14
mshA 575929 c.582C>T synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoB 760605 p.Ala267Thr missense_variant 0.13
rpoB 760979 c.1173G>A synonymous_variant 0.15
rpoB 761311 p.Pro502Leu missense_variant 0.13
rpoB 761479 p.Lys558Thr missense_variant 0.17
rpoB 761661 c.1855C>T synonymous_variant 0.2
rpoB 761710 p.Val635Asp missense_variant 0.25
rpoB 761713 p.Val636Asp missense_variant 0.25
rpoB 761899 p.Asp698Ala missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763641 p.Arg91Gln missense_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 763989 p.Gln207Pro missense_variant 0.15
rpoC 765232 c.1863G>A synonymous_variant 0.13
rpoC 765667 c.2298C>T synonymous_variant 0.18
rpoC 765673 p.Asp768Glu missense_variant 0.18
rpoC 766378 p.Ile1003Met missense_variant 0.18
rpoC 766460 p.Val1031Met missense_variant 0.33
rpoC 766820 p.Asp1151Asn missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776088 p.Val798Ala missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777456 p.Gly342Glu missense_variant 0.12
mmpR5 778043 c.-947G>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781841 c.282C>T synonymous_variant 0.12
fbiC 1304657 p.Ala576Gly missense_variant 0.13
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417042 c.306G>A synonymous_variant 0.25
embR 1417197 p.Gly51Arg missense_variant 0.12
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
fabG1 1673515 p.Gly26Arg missense_variant 0.14
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674928 p.Cys243Ser missense_variant 0.15
rpsA 1833867 p.Tyr109Ser missense_variant 0.11
rpsA 1834813 c.1272G>A synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102069 p.Ala325Val missense_variant 0.12
katG 2154711 c.1401G>A synonymous_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155452 c.660G>A synonymous_variant 0.22
katG 2155459 p.Asn218Thr missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169031 p.Asp528Asn missense_variant 0.2
PPE35 2169041 c.1572G>A synonymous_variant 0.6
PPE35 2169053 c.1560T>C synonymous_variant 1.0
PPE35 2169059 c.1554G>A synonymous_variant 0.75
PPE35 2169063 p.Met517Thr missense_variant 1.0
PPE35 2169065 p.Ala516Thr missense_variant 0.75
PPE35 2169068 c.1545G>T synonymous_variant 0.75
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223341 c.-177C>T upstream_gene_variant 0.13
pncA 2288746 p.Asp166Asn missense_variant 0.17
pncA 2289155 c.87C>T synonymous_variant 0.15
pncA 2289232 c.10T>C synonymous_variant 0.12
pncA 2289282 c.-41G>A upstream_gene_variant 0.12
pncA 2289318 c.-77G>T upstream_gene_variant 0.13
pncA 2289321 c.-81delC upstream_gene_variant 0.13
pncA 2289399 c.-158C>T upstream_gene_variant 0.14
pncA 2289526 c.-285T>C upstream_gene_variant 0.12
pncA 2289708 c.-467G>A upstream_gene_variant 0.13
pncA 2289975 c.-734G>T upstream_gene_variant 0.12
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518962 p.Asp283Gly missense_variant 0.11
kasA 2519048 p.Gly312Ser missense_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747136 p.Leu155Phe missense_variant 0.18
folC 2747214 p.Pro129Ser missense_variant 0.15
folC 2747435 p.Asp55Val missense_variant 0.12
folC 2747756 c.-158G>C upstream_gene_variant 0.2
folC 2747757 c.-159G>A upstream_gene_variant 0.2
thyX 3067836 p.Glu37Gly missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087778 p.Tyr320Cys missense_variant 0.29
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448859 p.Ala119Glu missense_variant 0.33
Rv3083 3449237 p.Arg245Lys missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474663 c.657C>T synonymous_variant 0.17
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568444 p.His79Arg missense_variant 0.22
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612674 p.Thr148Met missense_variant 0.2
Rv3236c 3612827 p.Ile97Asn missense_variant 0.25
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3640569 c.-966A>G upstream_gene_variant 0.12
fbiA 3640693 p.Ala51Thr missense_variant 0.17
fbiB 3641346 c.-189C>T upstream_gene_variant 0.17
rpoA 3877584 c.924C>T synonymous_variant 0.2
rpoA 3877825 p.Glu228Gly missense_variant 0.4
rpoA 3878567 c.-60C>G upstream_gene_variant 0.22
clpC1 4039167 p.Glu513Gly missense_variant 0.12
clpC1 4039336 c.1369C>T synonymous_variant 0.12
clpC1 4040051 c.654C>T synonymous_variant 0.22
clpC1 4040068 p.Val213Met missense_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4244235 c.1008_1011delGCTG frameshift_variant 0.17
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.17
embB 4246548 p.Pro12Gln missense_variant 0.22
embB 4246555 c.42G>C synonymous_variant 0.21
embB 4246556 p.Ala15Pro missense_variant 0.21
embB 4246563 p.Leu17Trp missense_variant 0.2
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248324 p.Ala604Gly missense_variant 0.29
embB 4249144 c.2631_2632insC frameshift_variant 0.12
aftB 4267501 p.Pro446Ser missense_variant 0.12
aftB 4267762 p.Asp359Asn missense_variant 0.14
aftB 4268017 p.Val274Met missense_variant 0.13
aftB 4268413 c.423delC frameshift_variant 0.17
aftB 4268917 c.-81C>T upstream_gene_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
aftB 4269645 c.-809C>T upstream_gene_variant 0.17
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ubiA 4270011 c.-178A>G upstream_gene_variant 0.14
ubiA 4270021 c.-188T>C upstream_gene_variant 0.11
ethA 4326103 c.1371G>C synonymous_variant 0.11
ethA 4326125 p.Gly450Asp missense_variant 0.12
ethA 4326710 p.Lys255Arg missense_variant 0.13
ethR 4326874 c.-675C>T upstream_gene_variant 0.17
ethA 4327596 c.-123G>A upstream_gene_variant 0.12
ethR 4327609 p.Ser21Pro missense_variant 0.12
whiB6 4338293 p.Ala77Thr missense_variant 0.17
whiB6 4338341 p.Leu61Val missense_variant 0.17
whiB6 4338345 c.176_177insA frameshift_variant 0.17
whiB6 4338348 p.Arg58* stop_gained 0.15
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407624 c.579G>C synonymous_variant 1.0
gid 4407798 c.405G>A synonymous_variant 1.0
gid 4407852 c.351G>C synonymous_variant 0.15
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408020 c.183C>T synonymous_variant 0.2