TB-Profiler result

Run: SRR6046659
Summary

Run ID: SRR6046659

Sample name:

Date: 04-04-2023 12:21:15

Number of reads: 578235

Percentage reads mapped: 98.46

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
katG 2155129 p.Trp328Leu missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 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 5135 c.-105G>T upstream_gene_variant 0.14
gyrB 5423 p.Ala62Thr missense_variant 0.14
gyrB 5875 p.Arg212Ser missense_variant 0.22
gyrB 6329 p.Glu364Lys missense_variant 0.2
gyrA 6625 c.-677G>T upstream_gene_variant 0.25
gyrB 6785 p.Glu516* stop_gained 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8008 p.Gly236Val missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490897 p.Asp39Tyr missense_variant 0.22
fgd1 490927 p.Gly49Cys missense_variant 0.2
fgd1 491521 c.739C>A synonymous_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575476 p.Asp43Glu missense_variant 1.0
mshA 575751 p.Gly135Val missense_variant 0.15
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576112 c.765C>A synonymous_variant 0.14
mshA 576467 p.Val374Leu missense_variant 0.29
mshA 576585 p.Arg413Leu missense_variant 0.13
mshA 576755 p.Arg470Ser missense_variant 0.5
ccsA 620492 p.Ser201Trp missense_variant 0.18
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.2
rpoB 759629 c.-178T>C upstream_gene_variant 0.17
rpoB 759855 p.Arg17Ser missense_variant 0.33
rpoB 760309 p.Val168Ala missense_variant 1.0
rpoB 761386 p.Ala527Val missense_variant 0.22
rpoB 762117 p.Ser771Ala missense_variant 0.13
rpoB 762326 p.Lys840Asn missense_variant 0.22
rpoC 762380 c.-990T>C upstream_gene_variant 0.4
rpoB 762825 p.Gly1007Trp missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763317 p.Leu1171Ile missense_variant 0.15
rpoC 764245 c.876C>A synonymous_variant 0.22
rpoC 764458 c.1089G>C synonymous_variant 0.12
rpoC 764461 c.1092A>G synonymous_variant 0.12
rpoC 764485 c.1116G>C synonymous_variant 0.12
rpoC 764491 c.1122G>T synonymous_variant 0.12
rpoC 764497 c.1128A>G synonymous_variant 0.12
rpoC 764500 c.1131C>G synonymous_variant 0.14
rpoC 764525 p.Arg386Ser missense_variant 0.18
rpoC 764842 p.Ile491Met missense_variant 0.13
rpoC 765232 c.1863G>C synonymous_variant 0.14
rpoC 765271 p.Lys634Asn missense_variant 0.17
rpoC 765284 p.Gln639Lys missense_variant 0.15
rpoC 766011 p.Ser881Tyr missense_variant 0.12
rpoC 766361 p.Val998Leu missense_variant 0.17
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766798 c.3429C>G synonymous_variant 0.11
rpoC 766857 p.Arg1163His missense_variant 0.33
rpoC 767148 p.Ala1260Gly missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775800 p.Ser894* stop_gained 0.33
mmpL5 775940 c.2541C>T synonymous_variant 0.18
mmpL5 775945 p.Val846Leu missense_variant 0.13
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776973 p.Met503Thr missense_variant 0.29
mmpL5 777501 p.Thr327Asn missense_variant 0.15
mmpL5 777526 p.Gly319Cys missense_variant 0.18
mmpS5 778588 p.Gln106His missense_variant 1.0
mmpS5 778614 p.Ser98Pro missense_variant 0.12
mmpR5 779335 p.Asp116Tyr missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 0.83
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303597 p.Phe223Ile missense_variant 0.25
fbiC 1303813 p.Phe295Leu missense_variant 0.29
fbiC 1304262 p.Trp444Cys missense_variant 0.4
fbiC 1304265 c.1335C>T synonymous_variant 0.4
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407154 c.186delC frameshift_variant 0.25
embR 1416841 c.507C>T synonymous_variant 0.29
embR 1417444 c.-97T>C upstream_gene_variant 0.25
atpE 1461079 p.Gly12Asp missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472863 n.1018T>C non_coding_transcript_exon_variant 1.0
rrs 1473329 n.1484G>C non_coding_transcript_exon_variant 0.75
rrl 1473832 n.175C>T non_coding_transcript_exon_variant 0.67
rrl 1473836 n.179A>T non_coding_transcript_exon_variant 0.5
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.5
rrl 1473862 n.205C>T non_coding_transcript_exon_variant 0.5
rrl 1476780 n.3123C>A non_coding_transcript_exon_variant 0.5
fabG1 1673723 p.Ala95Val missense_variant 0.17
inhA 1673982 c.-220G>T upstream_gene_variant 0.2
inhA 1674153 c.-49G>T upstream_gene_variant 0.17
rpsA 1833365 c.-177G>A upstream_gene_variant 0.25
rpsA 1833597 p.Ser19Asn missense_variant 0.13
rpsA 1833643 c.102C>T synonymous_variant 0.2
rpsA 1833779 p.Val80Phe missense_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834222 c.681T>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918711 p.Asp258Tyr missense_variant 0.12
ndh 2102875 c.168C>T synonymous_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154893 p.Glu407* stop_gained 0.18
katG 2155407 c.705G>T synonymous_variant 0.18
katG 2155446 c.666G>A synonymous_variant 0.13
katG 2156012 p.Gly34* stop_gained 0.15
PPE35 2167884 p.Gly910Asp missense_variant 0.67
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168041 p.Ala858Thr missense_variant 0.22
PPE35 2168898 p.Ala572Gly missense_variant 0.29
PPE35 2169351 p.Ala421Gly missense_variant 0.11
PPE35 2169724 p.Ile297Val missense_variant 0.12
PPE35 2169736 p.Gly293Ser missense_variant 0.12
PPE35 2170368 p.Gln82Arg missense_variant 0.22
PPE35 2170370 p.Thr81Ala missense_variant 0.22
PPE35 2170379 c.234G>T synonymous_variant 0.22
PPE35 2170382 c.231C>T synonymous_variant 0.22
PPE35 2170387 c.226C>T synonymous_variant 0.22
PPE35 2170403 c.210C>G synonymous_variant 0.22
PPE35 2170406 p.Ala69Glu missense_variant 0.22
PPE35 2170566 p.Phe16Tyr missense_variant 0.67
PPE35 2170792 c.-180T>C upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288968 p.Ala92Ser missense_variant 0.12
pncA 2289221 c.21C>A synonymous_variant 0.15
kasA 2517920 c.-195G>T upstream_gene_variant 0.5
kasA 2518048 c.-67C>G upstream_gene_variant 0.2
kasA 2518515 p.Pro134His missense_variant 0.4
kasA 2518639 c.525G>T synonymous_variant 1.0
eis 2714627 p.Ala236Ser missense_variant 0.13
eis 2714709 c.624C>A synonymous_variant 0.2
ahpC 2726338 p.Val49Gly missense_variant 0.33
folC 2746170 p.Ala477Ser missense_variant 0.14
folC 2746483 p.Phe372Leu missense_variant 0.13
folC 2746614 p.Gly329Arg missense_variant 0.33
folC 2746643 p.Arg319His missense_variant 0.33
folC 2746983 p.Gly206Ser missense_variant 0.17
folC 2747130 p.Ala157Ser missense_variant 0.33
pepQ 2859361 p.Glu353Ala missense_variant 0.12
pepQ 2859524 p.Gly299Cys missense_variant 0.18
pepQ 2859919 p.Arg167Leu missense_variant 0.17
ribD 2986976 c.138C>A synonymous_variant 0.12
ribD 2987231 c.393G>T synonymous_variant 0.15
ribD 2987362 p.Glu175Gly missense_variant 0.18
Rv2752c 3064578 c.1614C>A synonymous_variant 0.13
Rv2752c 3064721 p.His491Tyr missense_variant 0.14
Rv2752c 3064742 p.Gly484Cys missense_variant 0.14
Rv2752c 3064781 p.Gly471Ser missense_variant 0.17
Rv2752c 3065139 c.1053C>A synonymous_variant 0.12
Rv2752c 3065475 c.717C>A synonymous_variant 0.18
Rv2752c 3065539 p.Val218Glu missense_variant 0.2
Rv2752c 3065744 p.Thr150Ser missense_variant 0.14
Rv2752c 3065750 p.His148Asn missense_variant 0.17
Rv2752c 3067155 c.-964C>A upstream_gene_variant 0.33
thyX 3067393 p.Val185Leu missense_variant 0.33
thyX 3067621 p.Val109Leu missense_variant 0.15
thyX 3068047 c.-102C>A upstream_gene_variant 0.25
thyA 3074169 p.Trp101Cys missense_variant 0.14
thyA 3074280 c.192C>T synonymous_variant 0.17
thyA 3074645 c.-174T>G upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087247 p.Gln143Arg missense_variant 0.22
ald 3087732 p.Val305Met missense_variant 0.12
ald 3087910 p.Thr364Ile missense_variant 0.25
Rv3083 3448634 p.Thr44Asn missense_variant 0.22
Rv3083 3449016 c.513A>G synonymous_variant 0.18
Rv3083 3449207 p.Pro235Leu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474142 p.Trp46Arg missense_variant 0.18
fprA 3474160 p.Gly52Trp missense_variant 0.15
fprA 3474665 p.Gly220Val missense_variant 0.12
fprA 3474672 c.666C>T synonymous_variant 0.12
Rv3236c 3612433 c.684C>A synonymous_variant 0.5
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612867 p.Ser84Gly missense_variant 0.25
fbiB 3640572 c.-963C>T upstream_gene_variant 0.14
fbiA 3641276 p.Pro245Leu missense_variant 0.2
fbiB 3642789 p.Glu419Lys missense_variant 0.15
alr 3840270 p.Gly384Asp missense_variant 0.13
alr 3840706 p.Ala239Ser missense_variant 0.14
alr 3840716 c.705G>T synonymous_variant 0.14
alr 3840753 p.Arg223Leu missense_variant 0.18
alr 3840846 p.Gly192Glu missense_variant 0.4
alr 3841467 c.-48_-47insAGGC upstream_gene_variant 0.25
alr 3841475 c.-55C>A upstream_gene_variant 0.25
rpoA 3877675 p.Arg278Leu missense_variant 0.14
rpoA 3878190 c.318C>T synonymous_variant 0.33
rpoA 3878344 p.Arg55Leu missense_variant 0.12
ddn 3987166 p.Asp108Val missense_variant 0.15
clpC1 4039344 p.Glu454Gly missense_variant 0.15
clpC1 4040009 c.696C>A synonymous_variant 0.18
clpC1 4040150 c.555C>A synonymous_variant 0.12
clpC1 4040396 p.Ile103Met missense_variant 0.12
panD 4043993 p.Arg97Trp missense_variant 0.18
embC 4240586 p.Gly242Ser missense_variant 0.2
embC 4240862 p.Trp334Arg missense_variant 0.13
embC 4241619 p.Trp586Leu missense_variant 0.5
embC 4241786 c.1925delA frameshift_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242740 p.Leu960Ile missense_variant 0.18
embC 4243115 p.Leu1085Met missense_variant 0.17
embC 4243139 p.Arg1093Ser missense_variant 0.33
embA 4243410 p.Ala60Thr missense_variant 0.33
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243798 p.Val189Glu missense_variant 0.25
embA 4243953 p.Arg241Ser missense_variant 0.25
embA 4244184 p.Ser318Leu missense_variant 0.13
embA 4244240 p.Trp336* stop_gained 0.17
embA 4244429 c.1197G>T synonymous_variant 0.18
embA 4244445 c.1213C>T synonymous_variant 0.17
embA 4244750 c.1518C>A synonymous_variant 0.12
embA 4244771 c.1539G>T synonymous_variant 0.14
embA 4245377 c.2145T>C synonymous_variant 0.17
embB 4245677 c.-837G>T upstream_gene_variant 0.25
embA 4245987 p.Gln919Arg missense_variant 0.17
embA 4246477 p.Pro1082His missense_variant 0.15
embA 4246510 p.Leu1093Arg missense_variant 0.17
embB 4246532 c.19A>C synonymous_variant 0.22
embB 4247094 p.Gly194Glu missense_variant 0.25
embB 4247821 c.1308T>C synonymous_variant 0.12
embB 4247976 p.Val488Gly missense_variant 0.12
embB 4248173 p.Val554Leu missense_variant 0.22
embB 4248646 c.2133C>T synonymous_variant 0.14
embB 4248826 c.2313G>T synonymous_variant 0.25
embB 4248986 p.Gly825Cys missense_variant 0.14
embB 4249534 c.3021C>A synonymous_variant 0.29
aftB 4267002 p.Arg612Pro missense_variant 0.18
aftB 4267207 p.Val544Leu missense_variant 0.17
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268131 p.Val236Phe missense_variant 0.14
aftB 4268155 p.Arg228Trp missense_variant 0.22
aftB 4268728 p.Thr37Ser missense_variant 0.25
ethA 4326046 p.Glu476Asp missense_variant 0.12
ethA 4326120 p.Arg452Cys missense_variant 0.11
ethA 4326156 p.Leu440Met missense_variant 0.14
ethA 4326423 p.Gly351Trp missense_variant 0.18
ethR 4326679 c.-870C>A upstream_gene_variant 0.14
ethA 4326698 p.Arg259Leu missense_variant 0.17
ethA 4327361 p.Arg38Leu missense_variant 0.15
ethR 4327417 c.-132C>A upstream_gene_variant 0.14
ethA 4327905 c.-432C>A upstream_gene_variant 0.14
ethR 4327916 p.Ala123Val missense_variant 0.13
ethA 4328376 c.-903G>T upstream_gene_variant 0.13
ethA 4328464 c.-991C>G upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338654 c.-133A>G upstream_gene_variant 0.17
whiB6 4338719 c.-198T>A upstream_gene_variant 0.29
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407809 p.Asp132Tyr missense_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408256 c.-54G>T upstream_gene_variant 0.17