TB-Profiler result

Run: SRR7517720
Summary

Run ID: SRR7517720

Sample name:

Date: 04-04-2023 19:33:47

Number of reads: 768812

Percentage reads mapped: 85.18

Strain: lineage3.1.2.1

Drug-resistance: MDR-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
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 1.0
lineage3.1.2.1 East-African-Indian CAS2 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 761110 p.Asp435Val missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT frameshift_variant 1.0 ethionamide, ethionamide
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 5653 p.Glu138Asp missense_variant 0.18
gyrB 5769 p.Pro177His missense_variant 0.2
gyrB 7239 p.Ala667Asp missense_variant 0.2
gyrA 7250 c.-52C>A upstream_gene_variant 0.3
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8326 p.Gly342Val missense_variant 0.18
gyrA 8371 p.Arg357Leu missense_variant 0.29
gyrA 8610 p.Asp437Tyr missense_variant 0.22
gyrA 9164 c.1863G>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490845 c.63C>A synonymous_variant 0.22
fgd1 491172 c.390C>A synonymous_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575986 p.Leu213Phe missense_variant 0.23
mshA 576066 p.Pro240His missense_variant 0.18
mshA 576397 p.Ser350Arg missense_variant 0.18
ccsA 620202 c.312G>A synonymous_variant 0.4
ccsA 620293 p.Arg135Trp missense_variant 0.25
ccsA 620372 p.Ala161Asp missense_variant 0.33
ccsA 620541 c.651G>T synonymous_variant 0.33
ccsA 620718 c.828G>T synonymous_variant 0.25
rpoB 759619 c.-188C>A upstream_gene_variant 0.2
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 759900 p.Arg32Trp missense_variant 0.29
rpoB 760635 p.Pro277Thr missense_variant 0.18
rpoB 760934 c.1128C>A synonymous_variant 0.33
rpoB 760996 p.Arg397Leu missense_variant 0.25
rpoB 761364 p.Asp520Asn missense_variant 0.22
rpoB 761498 c.1692C>T synonymous_variant 0.33
rpoB 761814 p.Ala670Thr missense_variant 0.29
rpoB 762233 c.2427G>T synonymous_variant 0.21
rpoB 762246 p.Leu814Met missense_variant 0.2
rpoB 762432 p.Gly876Trp missense_variant 0.18
rpoB 762573 p.Gly923Ser missense_variant 0.4
rpoB 762576 p.Gln924Lys missense_variant 0.4
rpoB 762903 p.Asp1033Tyr missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764071 c.702G>T synonymous_variant 0.21
rpoC 764984 p.Asp539Tyr missense_variant 0.25
rpoC 765473 p.Glu702* stop_gained 0.33
rpoC 765896 p.Gly843Ser missense_variant 0.25
rpoC 766374 p.Ser1002Tyr missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776289 p.Gly731Asp missense_variant 0.33
mmpL5 776317 p.His722Asn missense_variant 0.29
mmpL5 776574 p.Ala636Glu missense_variant 0.18
mmpL5 777209 c.1272C>T synonymous_variant 0.22
mmpL5 777245 c.1236G>T synonymous_variant 0.29
mmpL5 777333 p.Gly383Val missense_variant 0.18
mmpL5 777604 p.Gln293* stop_gained 0.29
mmpL5 778231 p.Glu84* stop_gained 0.2
mmpL5 778241 p.Lys80Asn missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 0.83
rplC 801192 c.384G>A synonymous_variant 0.2
fbiC 1302771 c.-160G>A upstream_gene_variant 0.33
fbiC 1303647 c.717G>A synonymous_variant 0.25
fbiC 1303859 p.Gly310Val missense_variant 0.25
fbiC 1304128 p.Gln400* stop_gained 0.25
fbiC 1304609 p.Thr560Ile missense_variant 0.18
Rv1258c 1406539 p.Ala268Ser missense_variant 0.18
embR 1416304 c.1044C>T synonymous_variant 0.18
embR 1416750 p.Glu200Lys missense_variant 0.27
embR 1417250 p.Pro33His missense_variant 0.29
atpE 1461145 p.Ala34Glu missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>G non_coding_transcript_exon_variant 0.33
rrs 1472597 n.752G>T non_coding_transcript_exon_variant 0.4
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.4
rrs 1472707 n.862A>T non_coding_transcript_exon_variant 0.4
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrl 1474921 n.1264C>A non_coding_transcript_exon_variant 0.29
fabG1 1673151 c.-289C>A upstream_gene_variant 0.18
fabG1 1673506 p.Gly23* stop_gained 0.29
tlyA 1917972 c.33A>G synonymous_variant 0.91
tlyA 1918010 p.Ala24Val missense_variant 0.2
tlyA 1918023 c.84C>T synonymous_variant 0.25
ndh 2101912 c.1131G>T synonymous_variant 0.25
ndh 2102587 p.Leu152Phe missense_variant 0.25
ndh 2102969 p.Gly25Val missense_variant 0.25
katG 2154206 p.Ala636Ser missense_variant 0.18
katG 2154340 p.Ala591Glu missense_variant 0.25
katG 2154521 p.Ala531Thr missense_variant 0.5
katG 2154663 p.Phe483Leu missense_variant 0.29
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155227 p.Gln295His missense_variant 0.25
katG 2155383 c.729C>A synonymous_variant 0.22
katG 2155527 p.Glu195Asp missense_variant 0.18
katG 2155968 c.144G>A synonymous_variant 0.33
katG 2156057 p.Gly19Ser missense_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168235 p.Ala793Glu missense_variant 0.4
PPE35 2168238 p.Pro792Gln missense_variant 0.4
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2168712 p.Ala634Glu missense_variant 0.2
PPE35 2169968 c.645C>T synonymous_variant 0.22
PPE35 2169980 c.633C>T synonymous_variant 0.44
PPE35 2170004 c.609C>T synonymous_variant 0.29
PPE35 2170014 p.Gly200Val missense_variant 0.25
PPE35 2170348 p.Gln89Lys missense_variant 0.18
PPE35 2170681 c.-69G>A upstream_gene_variant 0.33
Rv1979c 2223050 p.Val39Met missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288771 c.471G>T synonymous_variant 0.2
pncA 2289011 c.231C>T synonymous_variant 0.4
pncA 2289042 p.Ser67* stop_gained 0.22
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289296 c.-55C>A upstream_gene_variant 0.22
pncA 2289339 c.-98C>A upstream_gene_variant 0.22
pncA 2289350 c.-109G>A upstream_gene_variant 0.22
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289713 c.-472C>A upstream_gene_variant 0.33
kasA 2518434 p.Arg107Gln missense_variant 0.4
kasA 2518498 c.384G>T synonymous_variant 0.22
kasA 2519115 p.Ala334Asp missense_variant 0.22
eis 2714320 p.Ala338Val missense_variant 0.25
eis 2714401 p.Ala311Val missense_variant 1.0
eis 2715087 c.246C>A synonymous_variant 0.27
eis 2715465 c.-133G>T upstream_gene_variant 0.22
eis 2715481 c.-149G>A upstream_gene_variant 0.18
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746932 p.Ala223Ser missense_variant 0.18
folC 2747532 p.Glu23* stop_gained 0.25
pepQ 2859541 p.Gly293Val missense_variant 0.22
pepQ 2859568 p.Ala284Val missense_variant 0.29
pepQ 2859644 p.Ala259Thr missense_variant 0.2
pepQ 2859915 c.504C>T synonymous_variant 0.29
pepQ 2859965 p.Ala152Ser missense_variant 0.27
pepQ 2860191 p.Glu76Asp missense_variant 0.29
pepQ 2860429 c.-11C>T upstream_gene_variant 0.18
ribD 2987214 p.Leu126Ile missense_variant 0.18
Rv2752c 3064701 p.Phe497Leu missense_variant 0.33
Rv2752c 3065625 c.567G>A synonymous_variant 0.22
Rv2752c 3065832 c.360C>A synonymous_variant 0.29
Rv2752c 3065948 p.Gly82Arg missense_variant 0.22
Rv2752c 3066156 c.36C>A synonymous_variant 0.22
thyX 3067432 p.Arg172Ser missense_variant 0.27
thyX 3067657 p.Arg97Trp missense_variant 0.2
thyX 3067759 p.His63Asn missense_variant 0.22
thyX 3067792 p.Pro52Ser missense_variant 0.2
thyA 3073893 c.579C>A synonymous_variant 0.25
thyA 3073907 p.Ala189Ser missense_variant 0.25
thyA 3074126 p.Leu116Met missense_variant 0.33
thyA 3074241 c.231C>A synonymous_variant 0.22
thyA 3074511 c.-40C>A upstream_gene_variant 0.29
thyA 3074525 c.-54C>A upstream_gene_variant 0.29
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086840 c.21C>T synonymous_variant 0.18
fbiD 3339272 p.Gly52Asp missense_variant 0.18
fbiD 3339761 c.644G>T stop_lost&splice_region_variant 0.4
Rv3083 3448343 c.-161C>T upstream_gene_variant 0.18
Rv3083 3448608 c.105G>A synonymous_variant 0.29
Rv3083 3448656 c.153G>A synonymous_variant 0.4
Rv3083 3449209 p.Asp236Tyr missense_variant 0.38
Rv3083 3449327 p.Arg275Leu missense_variant 0.33
Rv3083 3449538 c.1035G>T synonymous_variant 0.38
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474655 p.Asp217Asn missense_variant 0.33
fprA 3474700 p.Gly232Cys missense_variant 0.2
fprA 3474791 p.Pro262Gln missense_variant 0.22
fprA 3474835 p.Glu277Lys missense_variant 0.29
fprA 3475368 c.1362G>A synonymous_variant 0.25
Rv3236c 3612009 p.Ala370Ser missense_variant 0.2
Rv3236c 3612081 p.Ala346Thr missense_variant 0.22
Rv3236c 3612264 p.Gly285* stop_gained 0.43
Rv3236c 3613195 c.-79G>T upstream_gene_variant 0.22
fbiA 3640486 c.-57G>T upstream_gene_variant 0.22
fbiA 3640513 c.-30G>A upstream_gene_variant 0.29
fbiB 3640665 c.-870G>T upstream_gene_variant 0.33
fbiB 3640686 c.-849C>T upstream_gene_variant 0.18
fbiB 3641238 c.-297G>A upstream_gene_variant 0.4
fbiB 3641539 p.Thr2Ile missense_variant 0.5
fbiB 3642122 c.588C>T synonymous_variant 0.25
fbiB 3642703 p.Val390Ala missense_variant 0.25
alr 3840676 p.Asp249Tyr missense_variant 0.27
alr 3840779 c.642G>T synonymous_variant 0.15
alr 3841156 p.Leu89Ile missense_variant 0.14
rpoA 3877915 p.Thr198Asn missense_variant 0.2
ddn 3986828 c.-16C>A upstream_gene_variant 0.25
ddn 3987204 p.Glu121* stop_gained 0.25
clpC1 4038274 p.Gly811Cys missense_variant 0.25
clpC1 4038378 p.Thr776Ile missense_variant 0.29
clpC1 4038394 c.2308_2310delGCC conservative_inframe_deletion 0.22
clpC1 4038445 p.Ala754Ser missense_variant 0.33
clpC1 4038590 p.Phe705Leu missense_variant 0.33
clpC1 4038647 c.2057delG frameshift_variant 0.33
clpC1 4039541 c.1164C>A synonymous_variant 0.22
clpC1 4039676 p.Gln343His missense_variant 0.2
clpC1 4040339 p.Gln122His missense_variant 0.18
clpC1 4040840 c.-136G>T upstream_gene_variant 0.25
clpC1 4040852 c.-148C>A upstream_gene_variant 0.27
clpC1 4040880 c.-176G>T upstream_gene_variant 0.2
panD 4043936 p.Asp116Tyr missense_variant 0.22
panD 4044034 c.247delG frameshift_variant 0.2
panD 4044065 p.Gly73Cys missense_variant 0.18
panD 4044207 c.75G>T synonymous_variant 0.67
embC 4239946 c.84C>A synonymous_variant 0.22
embC 4240072 c.210C>A synonymous_variant 0.27
embC 4241196 p.Ser445* stop_gained 0.44
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242809 p.Leu983Met missense_variant 0.25
embC 4242836 p.Pro992Thr missense_variant 0.22
embA 4242967 c.-266C>T upstream_gene_variant 0.33
embC 4242998 p.Ala1046Ser missense_variant 0.22
embC 4243106 p.Arg1082Ser missense_variant 0.22
embA 4243264 p.Arg11Leu missense_variant 0.29
embA 4243781 c.549C>A synonymous_variant 0.4
embA 4244627 c.1395G>T synonymous_variant 0.25
embA 4245439 p.Ala736Val missense_variant 0.18
embB 4247935 c.1422C>A synonymous_variant 0.29
embB 4248745 c.2232C>A synonymous_variant 0.3
embB 4248858 p.Gly782Val missense_variant 0.25
embB 4249210 c.2697G>A synonymous_variant 0.4
aftB 4267384 p.Ala485Thr missense_variant 0.29
aftB 4267473 p.Gly455Val missense_variant 0.4
aftB 4267612 p.Asp409Tyr missense_variant 0.33
aftB 4267671 p.Ala389Glu missense_variant 0.22
aftB 4267764 p.Pro358Leu missense_variant 0.25
aftB 4268649 p.Trp63Leu missense_variant 0.2
ubiA 4269288 p.Phe182Leu missense_variant 0.25
ubiA 4269298 p.Ile179Thr missense_variant 1.0
ubiA 4269356 p.Arg160Ser missense_variant 0.2
ethA 4326068 p.Arg469Leu missense_variant 0.33
ethR 4326679 c.-870C>A upstream_gene_variant 0.25
ethA 4326762 p.Val238Ile missense_variant 0.25
ethA 4327126 p.Trp116Cys missense_variant 0.25
ethA 4327363 p.Lys37Asn missense_variant 0.67
ethR 4327796 p.Ala83Val missense_variant 0.33
ethA 4328139 c.-666G>T upstream_gene_variant 0.17
whiB6 4338307 p.Ala72Glu missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407591 p.Phe204Leu missense_variant 0.23
gid 4408087 p.Arg39His missense_variant 0.18
gid 4408098 c.105G>A synonymous_variant 0.22