TB-Profiler result

Run: SRR4035789
Summary

Run ID: SRR4035789

Sample name:

Date: 04-04-2023 07:17:56

Number of reads: 711418

Percentage reads mapped: 99.4

Strain: lineage4.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 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
pncA 2289090 p.His51Arg missense_variant 0.2 pyrazinamide
ahpC 2726142 c.-51G>T upstream_gene_variant 0.22 isoniazid
embB 4249071 p.Gln853Pro missense_variant 0.29 ethambutol
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 5582 p.Ala115Thr missense_variant 0.17
gyrB 5600 p.His121Tyr missense_variant 0.15
gyrB 5726 p.Pro163Ser missense_variant 0.22
gyrB 5732 p.Lys165Glu missense_variant 0.22
gyrB 6054 p.His272Arg missense_variant 0.29
gyrB 6179 p.Gly314Arg missense_variant 0.2
gyrB 6896 p.Arg553Trp missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7780 p.Val160Ala missense_variant 0.25
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 8341 p.Ala347Val missense_variant 0.13
gyrA 8771 p.His490Gln missense_variant 0.4
gyrA 8923 p.Gly541Asp missense_variant 0.15
gyrA 9285 p.Ala662Thr missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9708 c.2407T>C synonymous_variant 0.5
fgd1 490908 p.Gln42His missense_variant 0.17
fgd1 490994 p.Gly71Asp missense_variant 0.18
fgd1 491175 c.393G>A synonymous_variant 0.13
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575226 c.-122C>T upstream_gene_variant 0.33
mshA 575664 p.Gly106Ala missense_variant 0.25
ccsA 619806 c.-85G>T upstream_gene_variant 0.33
ccsA 620212 p.Gly108Ser missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760392 p.Val196Ile missense_variant 0.17
rpoB 760727 c.921C>T synonymous_variant 0.14
rpoB 761181 p.Arg459Cys missense_variant 0.14
rpoB 762637 c.2836delG frameshift_variant 0.18
rpoC 762686 c.-684G>A upstream_gene_variant 0.22
rpoC 764010 p.Arg214His missense_variant 0.33
rpoC 764147 p.Ser260Thr missense_variant 0.25
rpoC 764212 c.843C>T synonymous_variant 0.14
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764873 p.Pro502Ser missense_variant 0.29
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765312 p.Ala648Val missense_variant 0.18
rpoC 765353 p.Trp662Arg missense_variant 0.2
rpoC 765363 p.Glu665Gly missense_variant 0.2
rpoC 765616 c.2247C>T synonymous_variant 0.2
rpoC 765792 p.Thr808Ile missense_variant 0.17
rpoC 766042 p.Cys891* stop_gained 0.25
rpoC 766119 p.Glu917Gly missense_variant 0.18
rpoC 766132 p.Tyr921* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776015 c.2466C>A synonymous_variant 0.22
mmpL5 776407 p.Pro692Ser missense_variant 0.4
mmpL5 776408 c.2073G>T synonymous_variant 0.33
mmpL5 776511 p.Ser657Phe missense_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777694 p.Thr263Ala missense_variant 0.4
mmpL5 777721 p.Arg254Trp missense_variant 0.33
mmpL5 777752 c.729C>A synonymous_variant 0.29
mmpR5 778292 c.-698C>T upstream_gene_variant 0.2
mmpR5 778990 p.Val1Met missense_variant 0.25
mmpS5 779531 c.-626T>A upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781694 c.135G>A synonymous_variant 0.33
rpsL 781771 p.Gly71Ala missense_variant 0.33
rplC 801074 p.Ser89Leu missense_variant 0.29
fbiC 1303495 p.Pro189Ser missense_variant 0.33
fbiC 1303849 p.Pro307Ser missense_variant 0.15
fbiC 1305340 p.Ala804Thr missense_variant 0.2
Rv1258c 1406303 c.1038C>A synonymous_variant 0.33
Rv1258c 1406503 p.Val280Met missense_variant 0.12
Rv1258c 1407418 c.-78T>C upstream_gene_variant 0.13
embR 1416497 p.Ser284Trp missense_variant 0.4
embR 1416871 c.477C>A synonymous_variant 0.29
embR 1416940 c.408C>A synonymous_variant 0.22
embR 1416995 p.Glu118Gly missense_variant 0.22
embR 1417050 p.Gly100Ser missense_variant 0.2
embR 1417331 p.Thr6Ile missense_variant 0.33
atpE 1461005 c.-40G>C upstream_gene_variant 0.12
atpE 1461007 c.-38T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474879 n.1222G>A non_coding_transcript_exon_variant 0.22
rrl 1474899 n.1242T>C non_coding_transcript_exon_variant 0.29
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.4
rrl 1475931 n.2274C>T non_coding_transcript_exon_variant 0.13
rrl 1476177 n.2520G>T non_coding_transcript_exon_variant 0.18
rrl 1476432 n.2775T>C non_coding_transcript_exon_variant 0.13
fabG1 1673567 p.Ala43Val missense_variant 0.29
fabG1 1673707 p.Gly90Arg missense_variant 0.18
fabG1 1673819 p.Met127Thr missense_variant 0.29
fabG1 1673933 p.Arg165His missense_variant 0.17
inhA 1674345 p.Gln48His missense_variant 0.25
inhA 1674348 c.147C>T synonymous_variant 0.25
inhA 1674468 p.Asp89Glu missense_variant 0.29
inhA 1674572 p.Ala124Val missense_variant 0.25
rpsA 1834557 p.Ala339Val missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918606 p.Val223Leu missense_variant 0.29
tlyA 1918626 c.687G>A synonymous_variant 0.22
ndh 2101870 c.1173C>A synonymous_variant 0.2
ndh 2102801 p.Asn81Ser missense_variant 0.4
ndh 2102933 p.Asp37Gly missense_variant 0.29
katG 2154403 p.Gly570Ala missense_variant 0.17
katG 2154779 p.Val445Phe missense_variant 0.33
katG 2155145 p.Asn323Tyr missense_variant 0.2
katG 2155451 p.Ala221Thr missense_variant 0.33
katG 2155796 p.Ala106Thr missense_variant 0.22
katG 2155847 p.Pro89Ser missense_variant 0.13
PPE35 2168233 p.Ile794Phe missense_variant 0.17
PPE35 2168239 p.Pro792Thr missense_variant 0.18
PPE35 2168244 p.Ser790Asn missense_variant 0.18
PPE35 2168812 c.1800delC frameshift_variant 0.2
PPE35 2169100 p.Gly505Trp missense_variant 0.29
PPE35 2169320 p.Leu431Phe missense_variant 0.4
PPE35 2170085 c.528G>T synonymous_variant 0.33
PPE35 2170114 p.Ala167Thr missense_variant 0.29
Rv1979c 2221902 c.1263G>A synonymous_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518521 p.Lys136Met missense_variant 0.22
kasA 2518692 p.Ala193Val missense_variant 0.67
kasA 2519343 p.Ala410Val missense_variant 0.15
eis 2714586 c.747T>C synonymous_variant 0.5
eis 2714782 p.Gln184Leu missense_variant 0.4
eis 2714868 c.465C>T synonymous_variant 0.4
eis 2714872 p.Pro154Leu missense_variant 0.4
folC 2746528 c.1071C>T synonymous_variant 0.29
folC 2747136 p.Leu155Ile missense_variant 0.13
folC 2747152 p.Met149Ile missense_variant 0.15
folC 2747316 p.Arg95Gly missense_variant 0.33
folC 2747489 p.Arg37His missense_variant 0.15
folC 2747513 p.Gln29Leu missense_variant 0.17
folC 2747798 c.-200A>T upstream_gene_variant 0.4
pepQ 2859482 p.Ala313Ser missense_variant 0.25
pepQ 2860291 p.Leu43* stop_gained 0.18
pepQ 2860482 c.-64A>G upstream_gene_variant 0.14
Rv2752c 3065618 p.Gly192Cys missense_variant 0.29
Rv2752c 3065733 c.459G>A synonymous_variant 0.2
Rv2752c 3065901 c.291A>G synonymous_variant 0.22
Rv2752c 3066389 c.-198C>T upstream_gene_variant 0.15
thyX 3067526 c.420C>A synonymous_variant 0.25
thyX 3067610 p.Lys112Asn missense_variant 0.15
thyX 3067820 c.126C>T synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087486 p.Tyr223His missense_variant 0.33
fbiD 3339641 p.Ala175Asp missense_variant 0.5
Rv3083 3448355 c.-149C>A upstream_gene_variant 0.33
Rv3083 3448861 p.Gly120Ser missense_variant 0.33
Rv3083 3448988 p.Arg162Pro missense_variant 0.2
Rv3083 3449298 p.Met265Ile missense_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568524 c.156C>T synonymous_variant 0.18
whiB7 3568620 c.60C>T synonymous_variant 0.33
whiB7 3568675 p.Ser2Leu missense_variant 0.15
whiB7 3568859 c.-181delA upstream_gene_variant 0.4
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612427 c.690G>T synonymous_variant 0.17
fbiB 3641754 p.Arg74Cys missense_variant 0.25
fbiB 3641900 c.366G>C synonymous_variant 0.15
fbiB 3641955 p.Gly141Arg missense_variant 0.3
fbiB 3642313 p.Arg260His missense_variant 0.2
fbiB 3642325 p.Arg264His missense_variant 0.2
fbiB 3642339 p.Asp269Asn missense_variant 0.2
fbiB 3642762 p.Asp410Tyr missense_variant 0.25
alr 3840438 p.Val328Glu missense_variant 0.25
alr 3840456 p.Leu322Gln missense_variant 0.25
rpoA 3877553 p.Glu319* stop_gained 0.18
rpoA 3877884 c.624G>T synonymous_variant 0.22
rpoA 3878068 p.Val147Ala missense_variant 0.17
rpoA 3878072 p.Tyr146Asn missense_variant 0.18
rpoA 3878186 p.Gly108Ser missense_variant 0.29
rpoA 3878422 p.Gly29Glu missense_variant 0.25
rpoA 3878452 p.Ser19Tyr missense_variant 0.22
ddn 3987215 c.372A>G synonymous_variant 0.2
clpC1 4038234 p.Arg824Pro missense_variant 0.25
clpC1 4038522 p.Ile728Asn missense_variant 0.2
clpC1 4038573 p.Asn711Ser missense_variant 0.33
clpC1 4038937 p.Thr590Ala missense_variant 0.33
clpC1 4039283 c.1422C>T synonymous_variant 0.33
clpC1 4039751 p.Gln318His missense_variant 0.13
clpC1 4040237 c.468C>T synonymous_variant 0.33
panD 4044242 p.Thr14Ala missense_variant 0.29
panD 4044256 p.Lys9Thr missense_variant 0.25
embC 4239679 c.-184T>A upstream_gene_variant 0.22
embC 4240159 c.297C>T synonymous_variant 0.17
embC 4240236 p.Arg125Gln missense_variant 0.18
embC 4241037 p.Leu392Pro missense_variant 0.25
embC 4241065 c.1203C>T synonymous_variant 0.22
embC 4241074 c.1212G>A synonymous_variant 0.25
embC 4241083 c.1221G>A synonymous_variant 0.22
embC 4241435 p.Ala525Thr missense_variant 0.22
embC 4241673 p.Ala604Val missense_variant 0.33
embA 4242370 c.-863C>T upstream_gene_variant 0.4
embC 4242396 p.Pro845Leu missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4243044 p.Gln1061Leu missense_variant 0.15
embA 4244473 p.Val414Glu missense_variant 0.15
embA 4244479 p.Thr416Lys missense_variant 0.17
embA 4244720 p.Tyr496* stop_gained 0.17
embA 4245000 p.Phe590Ile missense_variant 0.29
embA 4245049 p.Tyr606Phe missense_variant 0.17
embA 4245052 p.Val607Ala missense_variant 0.14
embA 4245340 p.Gly703Asp missense_variant 0.2
embB 4246118 c.-396G>T upstream_gene_variant 0.2
embA 4246386 p.Arg1052Cys missense_variant 0.18
embB 4247100 p.Ala196Val missense_variant 0.4
embB 4249588 c.3075C>T synonymous_variant 0.13
embB 4249604 p.Gly1031Ser missense_variant 0.2
embB 4249613 p.Gly1034Ser missense_variant 0.18
embB 4249622 p.Leu1037Ile missense_variant 0.2
aftB 4267172 c.1665C>T synonymous_variant 0.2
aftB 4267561 p.Ala426Thr missense_variant 0.17
aftB 4267568 c.1269G>A synonymous_variant 0.15
aftB 4267636 p.Arg401Gly missense_variant 0.25
aftB 4269507 c.-671G>A upstream_gene_variant 0.15
ubiA 4269899 c.-66A>G upstream_gene_variant 0.17
ubiA 4269971 c.-138A>T upstream_gene_variant 0.29
ethA 4327725 c.-252C>G upstream_gene_variant 0.18
ethR 4328089 p.Arg181Trp missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407951 c.252G>T synonymous_variant 0.29