TB-Profiler result

Run: ERR2512512
Summary

Run ID: ERR2512512

Sample name:

Date: 31-03-2023 19:04:58

Number of reads: 621559

Percentage reads mapped: 99.61

Strain: lineage3

Drug-resistance: HR-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 0.99
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
katG 2154932 p.Thr394Ala missense_variant 0.1 isoniazid
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 6963 p.Arg575His missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8566 p.Ile422Asn missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491293 p.Pro171Thr missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491791 c.1009T>C stop_lost&splice_region_variant 0.11
mshA 576763 p.Trp472* stop_gained 0.25
ccsA 619733 c.-158G>A upstream_gene_variant 0.67
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763205 c.-165G>A upstream_gene_variant 1.0
rpoC 765588 p.Pro740Gln missense_variant 0.17
rpoC 766256 p.Arg963Cys missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776181 p.Asp767Ala missense_variant 1.0
mmpL5 778910 c.-430G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303008 p.Leu26Phe missense_variant 0.15
fbiC 1303212 c.282C>A synonymous_variant 0.11
fbiC 1304132 p.Ala401Val missense_variant 0.14
embR 1416510 p.Arg280Cys missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833759 p.Asp73Val missense_variant 0.12
tlyA 1917876 c.-64C>A upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155970 p.Leu48Met missense_variant 0.1
katG 2156523 c.-412G>A upstream_gene_variant 0.11
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168884 p.Gly577Ser missense_variant 0.14
PPE35 2169386 c.1227C>A synonymous_variant 0.17
PPE35 2169394 p.Ala407Ser missense_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.33
PPE35 2170497 p.Ala39Asp missense_variant 0.11
Rv1979c 2222470 p.Phe232Ser missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290040 c.-799A>T upstream_gene_variant 0.12
kasA 2519241 p.Pro376Arg missense_variant 0.18
kasA 2519326 c.1212C>T synonymous_variant 0.15
eis 2715355 c.-23G>T upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.23
ahpC 2726405 c.213C>A synonymous_variant 0.12
ahpC 2726410 p.Asp73Gly missense_variant 0.11
ribD 2987103 p.Arg89Cys missense_variant 0.12
Rv2752c 3065514 c.678C>T synonymous_variant 0.11
Rv2752c 3065567 p.Pro209Ala missense_variant 0.11
thyX 3067386 p.Gly187Asp missense_variant 0.13
thyX 3067486 p.Phe154Ile missense_variant 0.17
thyX 3067504 p.Ala148Thr missense_variant 0.18
thyA 3073818 c.654G>T synonymous_variant 0.11
thyA 3074645 c.-174T>G upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449771 p.Pro423Leu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474138 c.132T>C synonymous_variant 0.12
fprA 3474399 p.Trp131Cys missense_variant 0.11
Rv3236c 3612130 c.987G>A synonymous_variant 0.17
Rv3236c 3612375 p.Gly248Ser missense_variant 0.25
Rv3236c 3613143 c.-27A>G upstream_gene_variant 0.12
alr 3841052 c.369G>A synonymous_variant 0.11
alr 3841590 c.-170G>A upstream_gene_variant 1.0
rpoA 3878397 c.111G>C synonymous_variant 0.11
clpC1 4038917 c.1788C>T synonymous_variant 0.12
clpC1 4040138 c.567G>T synonymous_variant 0.12
clpC1 4040411 c.294T>G synonymous_variant 0.13
clpC1 4040841 c.-137C>T upstream_gene_variant 0.15
embC 4241155 c.1293C>T synonymous_variant 0.11
embC 4241303 p.Thr481Pro missense_variant 0.11
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244847 p.Gly539Cys missense_variant 0.17
embA 4244851 p.Arg540Leu missense_variant 0.17
embA 4245001 p.Phe590Ser missense_variant 0.13
embA 4245618 p.Asp796Asn missense_variant 0.12
embA 4246105 p.Pro958Gln missense_variant 0.15
embA 4246117 p.Pro962Gln missense_variant 0.15
embA 4246203 p.Arg991* stop_gained 0.17
embB 4247052 p.Asn180Thr missense_variant 0.11
embB 4249354 c.2841G>A synonymous_variant 0.15
embB 4249461 p.Pro983Leu missense_variant 0.2
aftB 4267577 p.His420Gln missense_variant 0.18
aftB 4268719 p.Asn40Asp missense_variant 1.0
ethA 4326366 p.Lys370Gln missense_variant 0.15
ethA 4326483 p.Arg331Cys missense_variant 0.22
ethA 4327016 p.Gly153Asp missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408144 p.Arg20Leu missense_variant 0.14