TB-Profiler result

Run: ERR2512938
Summary

Run ID: ERR2512938

Sample name:

Date: 31-03-2023 19:21:06

Number of reads: 571827

Percentage reads mapped: 99.5

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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 761106 p.Met434Val missense_variant 0.12 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 6326 p.Ser363Arg missense_variant 1.0
gyrB 6969 p.Asp577Gly missense_variant 0.15
gyrA 7315 p.Thr5Arg missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8091 p.Arg264Cys missense_variant 0.15
gyrA 8118 p.Glu273Lys missense_variant 0.12
gyrA 8790 p.Arg497Trp missense_variant 0.25
gyrA 9282 p.Gly661Arg missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490938 c.156G>A synonymous_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576115 c.768G>A synonymous_variant 0.12
ccsA 620463 c.573C>T synonymous_variant 0.15
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761301 p.Arg499Trp missense_variant 0.17
rpoB 761665 p.Val620Ala missense_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762881 p.Met1025Ile missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764113 c.744C>T synonymous_variant 0.22
rpoC 764360 p.Asp331Asn missense_variant 0.2
rpoC 764526 p.Arg386His missense_variant 0.13
rpoC 766307 p.Gly980Arg missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776015 c.2466C>T synonymous_variant 0.11
mmpL5 776042 c.2439C>T synonymous_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776223 p.Gly753Glu missense_variant 0.13
mmpL5 776255 c.2226C>A synonymous_variant 0.15
mmpL5 776867 c.1614G>T synonymous_variant 0.13
mmpL5 777643 p.Phe280Leu missense_variant 0.15
mmpL5 777944 c.537A>G synonymous_variant 0.25
mmpL5 778923 c.-443C>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800823 c.15C>A synonymous_variant 0.11
rplC 801063 c.255G>A synonymous_variant 0.12
rplC 801387 c.579G>A synonymous_variant 0.12
fbiC 1304706 c.1776C>T synonymous_variant 0.18
fbiC 1304716 p.Ala596Pro missense_variant 0.2
Rv1258c 1406156 c.1185C>A synonymous_variant 0.18
embR 1416639 p.Asp237Asn missense_variant 0.13
embR 1417188 p.Ala54Thr missense_variant 0.12
rrs 1471655 n.-191G>T upstream_gene_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833717 p.Thr59Ile missense_variant 0.17
rpsA 1834251 p.Val237Asp missense_variant 0.2
rpsA 1834444 c.903C>T synonymous_variant 0.14
rpsA 1834675 c.1134C>T synonymous_variant 0.14
tlyA 1917890 c.-50C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918186 p.Gly83Cys missense_variant 0.29
tlyA 1918399 p.Asp154Asn missense_variant 0.12
tlyA 1918684 p.Arg249Trp missense_variant 0.13
katG 2154187 p.Pro642Arg missense_variant 0.1
katG 2154642 c.1470C>G synonymous_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155722 c.390G>A synonymous_variant 0.17
PPE35 2167759 p.Gly952Ser missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169952 p.Asn221Asp missense_variant 0.22
PPE35 2170266 p.Gly116Asp missense_variant 0.12
PPE35 2170438 p.Gly59Ser missense_variant 0.15
PPE35 2170535 c.78G>T synonymous_variant 0.25
Rv1979c 2222821 p.Ser115Leu missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289393 c.-152C>A upstream_gene_variant 0.12
pncA 2290088 c.-847G>A upstream_gene_variant 0.22
kasA 2518263 p.Phe50Tyr missense_variant 1.0
kasA 2518801 c.687G>A synonymous_variant 0.13
kasA 2519093 p.Arg327Cys missense_variant 0.12
eis 2714445 p.Leu296Phe missense_variant 0.12
eis 2714955 c.378C>T synonymous_variant 0.25
eis 2715540 c.-208C>T upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.27
ahpC 2726529 p.Asp113Tyr missense_variant 0.12
folC 2746228 c.1371C>T synonymous_variant 0.22
folC 2747170 c.429T>A synonymous_variant 0.14
folC 2747226 p.Arg125Trp missense_variant 0.18
pepQ 2859449 p.Val324Met missense_variant 0.17
pepQ 2860237 p.Arg61His missense_variant 0.22
ribD 2986712 c.-127C>A upstream_gene_variant 0.25
ribD 2987104 p.Arg89His missense_variant 0.13
ribD 2987216 c.378T>C synonymous_variant 0.11
Rv2752c 3064670 p.Val508Leu missense_variant 0.29
thyX 3067265 c.681C>T synonymous_variant 0.4
thyX 3068026 c.-81G>A upstream_gene_variant 0.14
thyX 3068132 c.-187C>T upstream_gene_variant 0.25
thyA 3073934 p.Ser180Arg missense_variant 0.25
thyA 3074400 c.72C>T synonymous_variant 0.15
thyA 3074494 c.-23G>A upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448466 c.-38G>A upstream_gene_variant 0.25
Rv3083 3448779 c.276C>T synonymous_variant 0.14
Rv3083 3449033 p.Gly177Asp missense_variant 0.11
Rv3083 3449507 p.Arg335Gln missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474083 p.Ala26Val missense_variant 0.17
fprA 3474349 p.Pro115Ser missense_variant 0.13
fprA 3474481 p.Ala159Thr missense_variant 0.33
fprA 3474558 c.552A>G synonymous_variant 0.22
fbiB 3641638 p.Ala35Val missense_variant 0.2
fbiB 3642484 p.Trp317Ser missense_variant 0.15
fbiB 3642858 p.Ala442Thr missense_variant 0.11
alr 3840226 p.Thr399Ser missense_variant 0.13
alr 3840470 c.951C>T synonymous_variant 0.18
alr 3840562 p.Ile287Val missense_variant 0.11
alr 3840878 p.Gln181His missense_variant 0.12
alr 3840941 c.480C>T synonymous_variant 0.14
alr 3840986 c.435G>T synonymous_variant 0.18
alr 3841441 c.-22delG upstream_gene_variant 0.1
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3878162 p.Val116Ile missense_variant 0.14
rpoA 3878174 p.Pro112Ser missense_variant 0.14
rpoA 3878247 c.261G>T synonymous_variant 0.14
clpC1 4038269 c.2436C>T synonymous_variant 0.2
clpC1 4038773 p.Asp644Glu missense_variant 0.15
clpC1 4038776 p.Glu643Asp missense_variant 0.15
clpC1 4039074 p.Arg544His missense_variant 0.25
clpC1 4039765 p.Arg314Cys missense_variant 0.2
embC 4240356 p.Ala165Asp missense_variant 0.15
embC 4240468 c.606C>T synonymous_variant 0.15
embC 4241557 p.Ser565Arg missense_variant 0.11
embC 4241703 p.Arg614Leu missense_variant 0.25
embC 4242059 p.Ala733Thr missense_variant 0.4
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242739 c.-494C>A upstream_gene_variant 0.11
embA 4244348 p.Trp372Cys missense_variant 0.13
embA 4244407 p.Thr392Arg missense_variant 0.14
embA 4245094 p.Ile621Thr missense_variant 0.13
embB 4245995 c.-519G>A upstream_gene_variant 0.29
embB 4248324 p.Ala604Val missense_variant 0.14
embB 4248365 p.Val618Leu missense_variant 0.12
embB 4248386 c.1873C>A synonymous_variant 0.13
embB 4248407 p.Leu632Val missense_variant 0.15
embB 4248410 p.Phe633Leu missense_variant 0.15
embB 4248419 p.Leu636Met missense_variant 0.15
embB 4248425 c.1912T>C synonymous_variant 0.15
embB 4248430 c.1917T>C synonymous_variant 0.14
embB 4248432 p.Trp640Phe missense_variant 0.14
embB 4248839 p.Pro776Thr missense_variant 0.13
aftB 4267998 p.Leu280Ser missense_variant 0.12
aftB 4268350 p.Arg163Trp missense_variant 0.11
aftB 4268681 c.156C>G synonymous_variant 0.11
aftB 4268869 c.-33C>T upstream_gene_variant 0.22
aftB 4268870 c.-34G>T upstream_gene_variant 0.22
ubiA 4269933 c.-100C>T upstream_gene_variant 0.13
ethA 4326119 p.Arg452His missense_variant 0.2
ethR 4327084 c.-465G>A upstream_gene_variant 0.14
ethA 4327109 p.Ser122Ile missense_variant 0.18
ethR 4328077 p.Leu177Met missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407582 c.621T>C synonymous_variant 0.15
gid 4407588 c.615A>G synonymous_variant 1.0