TB-Profiler result

Run: ERR4816637
Summary

Run ID: ERR4816637

Sample name:

Date: 01-04-2023 14:32:37

Number of reads: 717514

Percentage reads mapped: 98.74

Strain: lineage4.3.3

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
katG 2155064 p.Ala350Ser missense_variant 0.22 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 5512 c.273C>A synonymous_variant 0.29
gyrB 5627 p.Ala130Ser missense_variant 0.12
gyrB 5778 p.Phe180Ser missense_variant 0.14
gyrB 6590 p.Arg451Ser missense_variant 0.15
gyrB 6623 p.Ser462Thr missense_variant 0.22
gyrB 6912 p.Asn558Ile missense_variant 0.18
gyrB 6985 p.Tyr582* stop_gained 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7804 p.Ser168Thr missense_variant 0.15
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 9036 p.Ala579Ser missense_variant 0.17
gyrA 9126 p.Ala609Thr missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9794 p.Asn831Lys missense_variant 0.2
fgd1 490633 c.-150C>A upstream_gene_variant 0.14
fgd1 491052 c.270C>T synonymous_variant 0.15
fgd1 491401 p.Leu207Met missense_variant 0.11
fgd1 491651 p.Pro290His missense_variant 0.13
mshA 576658 c.1311G>T synonymous_variant 0.17
ccsA 620315 c.427delG frameshift_variant 0.15
ccsA 620543 p.Arg218Leu missense_variant 0.22
rpoB 760590 p.Val262Phe missense_variant 0.15
rpoB 760723 p.Gly306Val missense_variant 0.22
rpoB 760862 c.1056G>T synonymous_variant 0.18
rpoB 760992 p.Glu396* stop_gained 0.29
rpoB 761418 p.Ala538Thr missense_variant 0.18
rpoB 762273 p.Ala823Ser missense_variant 0.22
rpoC 763442 p.Tyr25His missense_variant 0.2
rpoC 763771 c.402C>T synonymous_variant 0.67
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765097 p.Met576Ile missense_variant 0.5
rpoC 766265 p.Leu966Met missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776217 c.2258_2263delGATCCG disruptive_inframe_deletion 0.14
mmpL5 776495 c.1986G>T synonymous_variant 0.25
mmpL5 776947 p.Glu512Lys missense_variant 0.18
mmpL5 777983 c.498G>T synonymous_variant 0.13
mmpL5 778452 p.Thr10Met missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781697 c.138C>T synonymous_variant 0.2
fbiC 1303539 c.609G>A synonymous_variant 0.18
fbiC 1304373 p.His481Gln missense_variant 0.15
fbiC 1304400 c.1470C>A synonymous_variant 0.18
fbiC 1304572 p.Val548Phe missense_variant 0.14
fbiC 1304659 p.Tyr577Asn missense_variant 0.17
fbiC 1304736 p.Gln602His missense_variant 0.12
Rv1258c 1406124 p.Ala406Glu missense_variant 0.25
embR 1416387 p.Asp321Tyr missense_variant 0.15
embR 1417167 p.Glu61Gln missense_variant 0.14
embR 1417251 p.Pro33Thr missense_variant 0.12
atpE 1460915 c.-130C>T upstream_gene_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472494 n.649A>C non_coding_transcript_exon_variant 0.11
rrl 1473569 n.-89A>G upstream_gene_variant 0.13
rrl 1474122 n.465C>T non_coding_transcript_exon_variant 0.15
rrl 1474784 n.1127C>A non_coding_transcript_exon_variant 0.18
rrl 1474885 n.1228G>A non_coding_transcript_exon_variant 0.13
rrl 1474974 n.1317G>T non_coding_transcript_exon_variant 0.17
rrl 1475380 n.1723C>A non_coding_transcript_exon_variant 0.22
rrl 1475741 n.2086delT non_coding_transcript_exon_variant 0.33
rrl 1475837 n.2180C>T non_coding_transcript_exon_variant 0.13
rrl 1475882 n.2225C>A non_coding_transcript_exon_variant 0.13
inhA 1673484 c.-718C>A upstream_gene_variant 0.2
fabG1 1673585 p.Ser49Phe missense_variant 0.33
fabG1 1673987 p.Pro183Leu missense_variant 0.4
inhA 1674261 c.60G>T synonymous_variant 0.12
inhA 1674700 p.Ala167Ser missense_variant 0.12
inhA 1674930 p.Cys243* stop_gained 0.4
rpsA 1833725 p.Val62Leu missense_variant 0.22
rpsA 1834315 c.774C>A synonymous_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917998 p.Arg20Leu missense_variant 0.14
ndh 2101909 c.1134G>T synonymous_variant 0.22
ndh 2101919 p.Arg375Met missense_variant 0.22
ndh 2102627 p.Lys139Arg missense_variant 0.18
ndh 2102757 p.Gly96Trp missense_variant 0.33
katG 2154408 c.1704C>A synonymous_variant 0.17
katG 2154547 p.Glu522Gly missense_variant 0.15
katG 2154639 c.1473C>A synonymous_variant 0.14
katG 2154882 c.1230G>A synonymous_variant 0.29
katG 2155218 p.Leu298Phe missense_variant 0.14
katG 2156228 c.-117T>C upstream_gene_variant 0.12
PPE35 2167661 p.Ser984Arg missense_variant 0.17
PPE35 2167812 c.2800delC frameshift_variant 0.18
PPE35 2168246 c.2367C>T synonymous_variant 0.13
PPE35 2168776 p.Pro613Thr missense_variant 0.17
PPE35 2170068 p.Pro182Leu missense_variant 0.29
PPE35 2170787 c.-175T>C upstream_gene_variant 0.15
Rv1979c 2222366 p.Tyr267Asn missense_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223301 c.-138delG upstream_gene_variant 0.11
pncA 2288759 c.483G>T synonymous_variant 0.17
pncA 2289476 c.-235G>T upstream_gene_variant 0.18
pncA 2289481 c.-240G>T upstream_gene_variant 0.22
pncA 2289654 c.-413A>T upstream_gene_variant 0.17
pncA 2290235 c.-994G>T upstream_gene_variant 0.4
kasA 2518559 p.Gly149Cys missense_variant 0.2
kasA 2518919 p.Gly269Ser missense_variant 1.0
kasA 2519292 c.1180delT frameshift_variant 0.14
eis 2714487 c.846C>G synonymous_variant 0.15
eis 2715144 c.189G>C synonymous_variant 0.14
ahpC 2726576 p.Asp128Glu missense_variant 0.12
ahpC 2726630 p.Phe146Leu missense_variant 0.15
ahpC 2726691 p.Ala167Ser missense_variant 0.29
ahpC 2726743 p.Thr184Met missense_variant 0.12
folC 2746369 c.1230G>A synonymous_variant 0.2
folC 2746669 p.Glu310Asp missense_variant 0.29
pepQ 2859378 c.1041G>T synonymous_variant 0.12
ribD 2986661 c.-178G>C upstream_gene_variant 0.17
ribD 2986750 c.-89G>T upstream_gene_variant 0.29
ribD 2987246 c.408C>A synonymous_variant 0.18
ribD 2987515 p.Arg226Leu missense_variant 0.18
Rv2752c 3065226 c.966G>A synonymous_variant 0.17
Rv2752c 3065736 p.Asp152Glu missense_variant 0.2
thyX 3067751 c.195C>A synonymous_variant 0.12
thyX 3067790 c.156C>T synonymous_variant 0.12
thyX 3067911 p.Ile12Thr missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074639 c.-168G>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086861 p.Phe14Leu missense_variant 0.11
ald 3086881 p.Ala21Val missense_variant 0.12
ald 3087131 c.312C>A synonymous_variant 0.15
fbiD 3338922 c.-196G>A upstream_gene_variant 0.12
fbiD 3339015 c.-103T>C upstream_gene_variant 0.15
fbiD 3339048 c.-70C>G upstream_gene_variant 0.15
fbiD 3339138 c.21C>T synonymous_variant 0.2
fbiD 3339747 c.630G>T synonymous_variant 0.2
Rv3083 3448540 p.Gly13Ser missense_variant 0.15
Rv3083 3449411 p.Gly303Val missense_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474261 c.255C>A synonymous_variant 0.12
fprA 3475066 p.Glu354Lys missense_variant 0.12
fprA 3475305 c.1299C>A synonymous_variant 0.15
fprA 3475361 c.1357_1360delATTG frameshift_variant 0.18
whiB7 3568635 p.Leu15Phe missense_variant 0.17
Rv3236c 3612009 p.Ala370Ser missense_variant 0.2
Rv3236c 3612281 p.Gly279Asp missense_variant 0.17
Rv3236c 3612304 c.813C>A synonymous_variant 0.17
Rv3236c 3612450 c.667C>T synonymous_variant 0.29
Rv3236c 3612969 p.Gly50Trp missense_variant 0.13
fbiA 3640409 c.-134C>A upstream_gene_variant 0.22
fbiB 3641961 p.Thr143Ala missense_variant 0.15
fbiB 3642148 p.Val205Ala missense_variant 0.33
fbiB 3642618 p.Asp362Asn missense_variant 0.2
fbiB 3642707 c.1173C>A synonymous_variant 0.18
alr 3840271 p.Gly384Cys missense_variant 0.5
alr 3841054 p.Ala123Ser missense_variant 0.14
alr 3841238 c.183G>A synonymous_variant 0.25
alr 3841422 c.-2C>A upstream_gene_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039247 p.Glu486Asp missense_variant 0.29
panD 4043897 p.Gly129Ser missense_variant 0.15
embC 4239719 c.-144G>T upstream_gene_variant 0.2
embC 4240066 c.204C>A synonymous_variant 0.25
embC 4240799 p.Tyr313Asn missense_variant 0.14
embC 4241034 p.Pro391Leu missense_variant 0.33
embC 4241506 c.1644G>T synonymous_variant 0.11
embC 4241739 p.Val626Glu missense_variant 0.18
embC 4241911 c.2049C>A synonymous_variant 0.4
embC 4242182 p.Ala774Ser missense_variant 1.0
embC 4242324 p.Gly821Val missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245332 c.2100C>A synonymous_variant 0.12
embA 4246069 p.Pro946Gln missense_variant 0.25
embA 4246129 p.Ser966Tyr missense_variant 0.15
embB 4246419 c.-95C>T upstream_gene_variant 0.13
embA 4246509 p.Leu1093Met missense_variant 0.14
embB 4246849 p.Gln112His missense_variant 0.17
embB 4247239 p.Leu242Phe missense_variant 0.12
embB 4248818 p.Gly769Cys missense_variant 0.17
embB 4248964 c.2451G>A synonymous_variant 0.22
embB 4249802 p.Gly1097Cys missense_variant 0.25
aftB 4266954 c.1883G>A splice_region_variant&stop_retained_variant 0.18
aftB 4267487 p.Leu450Phe missense_variant 0.22
aftB 4268040 p.Leu266Pro missense_variant 1.0
aftB 4268060 p.Asn259Lys missense_variant 0.11
aftB 4268135 c.702G>T synonymous_variant 0.29
ubiA 4269221 p.Ala205Thr missense_variant 0.13
aftB 4269516 c.-680G>A upstream_gene_variant 0.15
aftB 4269531 c.-695G>A upstream_gene_variant 0.18
ethA 4326297 p.Leu393Met missense_variant 0.17
ethA 4326701 p.Arg258Gln missense_variant 0.17
ethR 4327974 p.Met142Ile missense_variant 0.15
ethA 4328079 c.-606C>A upstream_gene_variant 0.2
ethR 4328114 p.Gly189Val missense_variant 0.15
whiB6 4338479 p.Phe15Ile missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407902 p.Leu101Ile missense_variant 0.22
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408451 c.-249T>C upstream_gene_variant 0.18