TB-Profiler result

Run: ERR6336753
Summary

Run ID: ERR6336753

Sample name:

Date: 02-04-2023 02:02:09

Number of reads: 1391481

Percentage reads mapped: 99.05

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
rpoC 765572 p.Asp735Asn missense_variant 0.17 rifampicin
pncA 2288779 p.Val155Met missense_variant 0.13 pyrazinamide
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7930 p.Ala210Gly missense_variant 0.11
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 9287 c.1986G>A synonymous_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490870 p.His30Tyr missense_variant 0.2
fgd1 490918 p.His46Tyr missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575344 c.-4A>G upstream_gene_variant 0.1
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 575464 c.117G>A synonymous_variant 0.15
mshA 575863 c.516G>A synonymous_variant 0.13
rpoB 760889 c.1083C>T synonymous_variant 0.2
rpoB 761152 p.Leu449Gln missense_variant 0.33
rpoB 761535 p.Pro577Ser missense_variant 0.22
rpoB 761602 p.Ala599Val missense_variant 0.25
rpoB 761710 p.Val635Asp missense_variant 0.14
rpoB 761713 p.Val636Asp missense_variant 0.14
rpoB 762264 p.Gly820Ser missense_variant 0.13
rpoC 762741 c.-629C>T upstream_gene_variant 0.2
rpoB 762777 p.Asp991Asn missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763682 p.Trp105Arg missense_variant 0.1
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764299 p.Met310Ile missense_variant 0.14
rpoC 766092 p.Gly908Ala missense_variant 0.4
rpoC 766276 c.2907C>G synonymous_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777616 p.Arg289Cys missense_variant 0.15
mmpL5 778437 p.Pro15Leu missense_variant 0.29
mmpS5 778649 p.Leu86Pro missense_variant 0.12
mmpR5 779177 p.Ser63Ile missense_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781759 p.Ile67Thr missense_variant 0.17
rplC 801010 p.Gly68Ser missense_variant 0.17
fbiC 1304103 c.1173G>A synonymous_variant 0.13
fbiC 1304302 p.Arg458Cys missense_variant 1.0
Rv1258c 1406142 c.1197_1198delGC frameshift_variant 0.25
Rv1258c 1406311 c.1030C>T synonymous_variant 0.18
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0
Rv1258c 1406729 c.610_611delCG frameshift_variant 0.12
embR 1416423 p.Arg309Gly missense_variant 0.15
embR 1416982 c.366C>T synonymous_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417028 p.Asp107Val missense_variant 0.14
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673554 p.Gly39Arg missense_variant 0.25
fabG1 1673560 p.Lys41Leu missense_variant 0.29
fabG1 1673636 p.Asp66Gly missense_variant 0.13
inhA 1674162 c.-40C>T upstream_gene_variant 1.0
inhA 1674403 p.Glu68Lys missense_variant 0.17
rpsA 1834489 c.948T>C synonymous_variant 0.11
rpsA 1834815 p.His425Pro missense_variant 0.13
rpsA 1834908 p.Ser456Trp missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102092 c.951G>A synonymous_variant 0.13
ndh 2102106 p.Gly313Arg missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156376 c.-265C>T upstream_gene_variant 0.13
katG 2156443 c.-332C>T upstream_gene_variant 0.13
katG 2156484 c.-373A>G upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288734 p.Ala170Thr missense_variant 0.14
pncA 2289357 c.-116G>A upstream_gene_variant 0.14
pncA 2289845 c.-604G>C upstream_gene_variant 0.11
pncA 2289879 c.-638G>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714812 p.Glu174Ala missense_variant 0.14
eis 2715491 c.-159G>A upstream_gene_variant 0.18
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746136 c.1463G>A splice_region_variant&stop_retained_variant 0.15
pepQ 2859914 p.Glu169Lys missense_variant 0.18
pepQ 2859971 p.Ala150Thr missense_variant 0.13
pepQ 2860221 c.198G>T synonymous_variant 0.33
ribD 2986691 c.-148G>A upstream_gene_variant 0.14
ribD 2987113 p.Gly92Ala missense_variant 0.11
ribD 2987338 p.Gly167Asp missense_variant 0.4
ribD 2987394 p.Gly186Ser missense_variant 0.5
Rv2752c 3064632 c.1560C>T synonymous_variant 0.13
Rv2752c 3064822 p.Val457Ala missense_variant 0.17
Rv2752c 3064825 p.Asp456Val missense_variant 0.17
Rv2752c 3064828 p.Gly455Asp missense_variant 0.2
Rv2752c 3065622 c.570G>A synonymous_variant 0.17
thyX 3067441 p.Gln169Lys missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087761 c.942C>T synonymous_variant 0.15
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449126 p.Thr208Met missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474099 c.93C>T synonymous_variant 0.2
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.98
whiB7 3568431 c.249C>G synonymous_variant 0.29
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612578 p.Glu180Val missense_variant 0.15
Rv3236c 3612682 c.435C>T synonymous_variant 0.14
Rv3236c 3612809 p.Pro103Leu missense_variant 0.12
Rv3236c 3612818 c.297_298delCA frameshift_variant 0.14
Rv3236c 3612854 p.His88Pro missense_variant 0.22
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiB 3641624 p.Ser30Arg missense_variant 0.2
fbiB 3642166 p.Ala211Gly missense_variant 0.15
alr 3840443 c.978G>A synonymous_variant 0.22
alr 3841104 p.Thr106Ile missense_variant 0.13
rpoA 3877631 p.Ser293Thr missense_variant 0.12
rpoA 3877748 c.760C>T synonymous_variant 0.2
rpoA 3877896 c.612G>A synonymous_variant 0.2
clpC1 4038851 c.1854G>A synonymous_variant 0.14
clpC1 4038887 c.1818G>A synonymous_variant 0.2
clpC1 4038914 c.1791G>A synonymous_variant 0.2
clpC1 4039048 p.Gly553Ser missense_variant 0.17
clpC1 4039746 p.Ile320Ser missense_variant 0.17
clpC1 4040090 c.615T>C synonymous_variant 0.11
clpC1 4040093 c.612C>G synonymous_variant 0.1
clpC1 4040181 p.Gly175Asp missense_variant 0.17
clpC1 4040183 c.522C>T synonymous_variant 0.14
clpC1 4040257 p.Ala150Thr missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240481 p.Pro207Ser missense_variant 0.15
embC 4240571 p.Gly237Trp missense_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240962 p.Leu367Pro missense_variant 0.14
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242175 c.2313G>C synonymous_variant 0.22
embC 4242525 p.Ala888Val missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243580 c.348G>A synonymous_variant 1.0
embA 4243939 p.Trp236* stop_gained 0.2
embA 4243941 p.Leu237Met missense_variant 0.18
embA 4244184 p.Ser318Arg missense_variant 0.14
embA 4244194 p.Gly321Ala missense_variant 0.2
embA 4244350 p.Leu373Pro missense_variant 0.12
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245427 p.Ser732Thr missense_variant 0.13
embA 4245829 p.Arg866Pro missense_variant 0.25
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.42
embB 4246548 p.Pro12Gln missense_variant 0.41
embB 4246555 c.42G>C synonymous_variant 0.38
embB 4246556 p.Ala15Pro missense_variant 0.3
embB 4246563 p.Leu17Trp missense_variant 0.29
embB 4246584 p.Arg24Pro missense_variant 0.17
embB 4247244 p.Gly244Glu missense_variant 0.13
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247704 c.1191G>A synonymous_variant 0.12
embB 4248323 p.Ala604Thr missense_variant 0.18
embB 4248745 c.2232C>G synonymous_variant 0.14
embB 4249384 c.2871G>A synonymous_variant 0.67
aftB 4267454 c.1383C>T synonymous_variant 0.25
aftB 4267736 c.1101C>T synonymous_variant 0.12
aftB 4268020 p.Ser273Pro missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269864 c.-32delG upstream_gene_variant 1.0
ethA 4326764 p.Ala237Val missense_variant 0.18
ethA 4326777 p.Met233Leu missense_variant 0.12
ethR 4327583 p.Pro12Leu missense_variant 0.15
ethR 4327630 p.Ala28Thr missense_variant 0.13
ethR 4327994 p.Thr149Met missense_variant 0.12
ethA 4328385 c.-912G>A upstream_gene_variant 0.12
whiB6 4338239 c.283C>T synonymous_variant 0.2
whiB6 4338289 p.Gly78Glu missense_variant 0.33
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338599 c.-78A>C 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 4407873 c.330G>T synonymous_variant 1.0