TB-Profiler result

Run: SRR6896396
Summary

Run ID: SRR6896396

Sample name:

Date: 04-04-2023 18:04:43

Number of reads: 432031

Percentage reads mapped: 99.42

Strain: lineage4.3.2.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.99
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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 761196 p.Leu464Met missense_variant 0.14 rifampicin
tlyA 1918614 c.677delA frameshift_variant 0.13 capreomycin
katG 2155128 p.Trp328Cys missense_variant 0.25 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 5520 p.Pro94Leu missense_variant 1.0
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9344 c.2043C>A synonymous_variant 0.14
gyrA 9424 p.Asp708Gly missense_variant 0.12
gyrA 9581 c.2281delA frameshift_variant 0.14
gyrA 9695 c.2394C>A synonymous_variant 0.12
gyrA 9715 p.Asn805Ser missense_variant 0.15
fgd1 491670 p.Lys296Asn missense_variant 0.11
mshA 575271 c.-77C>G upstream_gene_variant 0.18
mshA 575705 c.358T>C synonymous_variant 0.12
mshA 575859 p.Val171Ala missense_variant 0.11
mshA 576113 c.766C>A synonymous_variant 0.2
mshA 576407 p.Ser354Pro missense_variant 0.2
mshA 576541 p.Trp398Cys missense_variant 0.17
mshA 576602 c.1255C>A synonymous_variant 0.13
ccsA 620056 p.Thr56Ala missense_variant 0.17
ccsA 620359 p.Tyr157His missense_variant 0.12
ccsA 620411 p.Ile174Thr missense_variant 0.13
ccsA 620683 p.Glu265* stop_gained 0.12
rpoB 761146 p.Arg447Leu missense_variant 0.12
rpoB 761419 p.Ala538Asp missense_variant 0.17
rpoB 761666 c.1860G>C synonymous_variant 0.15
rpoB 762609 p.His935Asn missense_variant 0.17
rpoC 762719 c.-651C>T upstream_gene_variant 0.17
rpoB 762802 p.Asp999Gly missense_variant 0.22
rpoB 762948 p.Gln1048Lys missense_variant 0.13
rpoC 763733 p.Pro122Thr missense_variant 0.12
rpoC 763904 p.Ala179Ser missense_variant 0.18
rpoC 763912 c.543G>C synonymous_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765585 p.Pro739Leu missense_variant 0.14
rpoC 767304 p.Tyr1312Cys missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776327 c.2154C>T synonymous_variant 0.12
mmpL5 776345 c.2136C>T synonymous_variant 0.14
mmpL5 776624 p.Asn619Lys missense_variant 0.13
mmpL5 776825 c.1656A>G synonymous_variant 0.12
mmpL5 776866 p.Met539Leu missense_variant 0.13
mmpL5 777921 p.Thr187Ile missense_variant 0.12
mmpL5 778092 p.Trp130Leu missense_variant 0.12
mmpR5 779152 p.Glu55Gln missense_variant 0.15
mmpL5 779272 c.-792A>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302966 c.36G>T synonymous_variant 0.12
fbiC 1303057 p.Glu43* stop_gained 0.17
fbiC 1303512 c.582T>G synonymous_variant 0.12
fbiC 1303788 c.858T>C synonymous_variant 0.1
Rv1258c 1406120 c.1221C>A synonymous_variant 0.18
Rv1258c 1406360 c.981C>A synonymous_variant 0.13
Rv1258c 1406382 p.Val320Ala missense_variant 0.11
Rv1258c 1406493 p.Ile283Thr missense_variant 0.12
Rv1258c 1406560 p.Gly261Cys missense_variant 0.12
Rv1258c 1407475 c.-135G>T upstream_gene_variant 0.13
embR 1416246 p.His368Asn missense_variant 0.12
embR 1416309 p.Ser347Pro missense_variant 0.1
embR 1417255 c.93C>T synonymous_variant 0.13
embR 1417506 c.-159T>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 1.0
rrl 1473932 n.280_283delCGCA non_coding_transcript_exon_variant 0.12
rrl 1473988 n.331T>C non_coding_transcript_exon_variant 0.11
rrl 1475826 n.2169T>C non_coding_transcript_exon_variant 0.11
fabG1 1674174 p.Met245Ile missense_variant 0.13
inhA 1674438 c.237C>T synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154467 p.Cys549Arg missense_variant 0.1
katG 2154497 p.Ser539Pro missense_variant 0.13
katG 2155517 p.Gly199Cys missense_variant 0.17
PPE35 2167671 p.Phe981Ser missense_variant 0.25
PPE35 2168253 p.Pro787Arg missense_variant 0.11
PPE35 2168330 c.2283G>T synonymous_variant 0.13
PPE35 2168813 c.1722_1799delAGCGCTAGGTGCGTTCAATCTGCCGACGCTGAGTATTCCGTCGGTGACGGTTCCGCCGATCACGATTCCGGCTGGCAC disruptive_inframe_deletion 1.0
PPE35 2169531 p.Phe361Ser missense_variant 0.11
PPE35 2169787 p.Asn276Tyr missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517961 c.-153_-151delCGC upstream_gene_variant 0.17
kasA 2518623 p.Ala170Val missense_variant 0.18
kasA 2519181 c.1068delG frameshift_variant 0.2
eis 2714807 p.Glu176* stop_gained 0.17
eis 2714822 p.His171Tyr missense_variant 0.18
eis 2714880 c.453C>A synonymous_variant 0.18
folC 2746415 p.Glu395Val missense_variant 1.0
folC 2746499 p.Ala367Glu missense_variant 0.18
folC 2746676 p.Ser308Tyr missense_variant 0.2
folC 2746686 p.Ala305Ser missense_variant 0.2
folC 2746872 p.Glu243* stop_gained 0.14
folC 2747099 p.Pro167Leu missense_variant 0.14
folC 2747140 p.Glu153Asp missense_variant 0.13
folC 2747649 c.-51C>A upstream_gene_variant 0.12
ribD 2986868 c.30T>C synonymous_variant 0.12
ribD 2987227 p.Met130Lys missense_variant 0.15
Rv2752c 3064724 p.Pro490Thr missense_variant 0.13
Rv2752c 3065272 p.Thr307Ile missense_variant 0.13
Rv2752c 3065442 c.750T>C synonymous_variant 0.18
Rv2752c 3065755 p.Val146Ala missense_variant 0.11
thyX 3067684 p.Ser88Pro missense_variant 0.14
thyX 3068051 c.-106A>G upstream_gene_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074515 c.-44T>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087152 c.333C>A synonymous_variant 0.2
ald 3087446 c.627C>A synonymous_variant 0.12
fbiD 3339016 c.-102G>T upstream_gene_variant 0.33
Rv3083 3448790 p.Glu96Gly missense_variant 0.17
Rv3083 3448878 c.375C>T synonymous_variant 0.2
Rv3083 3448921 p.Thr140Ala missense_variant 0.17
Rv3083 3449985 c.1482G>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474259 p.Gly85Cys missense_variant 0.18
fprA 3474731 p.Gly242Val missense_variant 0.13
fprA 3474738 c.732C>A synonymous_variant 0.14
fprA 3474874 p.Gly290Ser missense_variant 0.18
fprA 3475136 p.Asp377Gly missense_variant 0.12
Rv3236c 3612119 p.Arg333Leu missense_variant 0.14
Rv3236c 3613251 c.-135C>A upstream_gene_variant 0.14
fbiA 3641201 p.Ile220Thr missense_variant 0.13
fbiB 3642066 p.Gly178Cys missense_variant 0.13
fbiB 3642131 c.597C>A synonymous_variant 0.13
fbiB 3642413 c.879G>T synonymous_variant 0.25
fbiB 3642484 p.Trp317Leu missense_variant 0.15
rpoA 3877575 c.933C>T synonymous_variant 0.14
rpoA 3877615 p.Lys298Arg missense_variant 0.12
rpoA 3878251 p.Ser86Phe missense_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039039 p.Gly556Ser missense_variant 0.14
clpC1 4040083 p.Thr208Ser missense_variant 0.12
clpC1 4040296 p.Gln137Lys missense_variant 0.15
panD 4044294 c.-13A>G upstream_gene_variant 0.17
panD 4044382 c.-102delC upstream_gene_variant 0.18
embC 4240589 p.Ala243Thr missense_variant 0.12
embC 4240643 c.781C>A synonymous_variant 0.15
embC 4241266 c.1404C>T synonymous_variant 0.13
embC 4242477 p.Pro872His missense_variant 0.18
embA 4242634 c.-599G>A upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242665 p.Ala935Thr missense_variant 0.33
embC 4243031 p.Trp1057Arg missense_variant 0.12
embC 4243079 p.Ala1073Pro missense_variant 0.11
embA 4243389 p.Gly53Ser missense_variant 0.12
embA 4243494 p.Leu88Met missense_variant 0.14
embA 4243613 c.381C>A synonymous_variant 0.15
embA 4245658 p.Ser809Tyr missense_variant 0.18
embA 4245991 p.Pro920His missense_variant 0.14
embA 4246239 p.Pro1003Thr missense_variant 0.29
embB 4246919 p.Pro136Ser missense_variant 0.12
embB 4247071 c.558C>T synonymous_variant 0.12
embB 4247705 p.Phe398Leu missense_variant 0.15
embB 4249013 p.Pro834Thr missense_variant 0.25
aftB 4266986 c.1851T>C synonymous_variant 0.17
aftB 4267139 c.1698G>A synonymous_variant 0.13
aftB 4267190 c.1646dupG frameshift_variant 0.17
aftB 4268105 c.732T>C synonymous_variant 0.2
aftB 4268129 c.708T>C synonymous_variant 0.18
aftB 4268151 p.Met229Thr missense_variant 0.18
aftB 4268425 p.Gly138Cys missense_variant 0.22
aftB 4268694 p.Val48Ala missense_variant 0.18
aftB 4268871 c.-35G>T upstream_gene_variant 0.12
ubiA 4269557 p.Ala93Ser missense_variant 0.12
ethA 4327350 p.Gly42Cys missense_variant 0.12
ethA 4327780 c.-307G>T upstream_gene_variant 0.15
ethA 4328261 c.-788C>A upstream_gene_variant 0.12
ethA 4328320 c.-847C>T upstream_gene_variant 0.17
whiB6 4338288 c.234G>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407854 p.Gly117Trp missense_variant 0.14
gid 4407936 c.267T>C synonymous_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 1.0
PPE35 2168813 c.1721_1799delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC frameshift_variant 1.0