TB-Profiler result

Run: ERR1750921
Summary

Run ID: ERR1750921

Sample name:

Date: 31-03-2023 14:59:47

Number of reads: 860045

Percentage reads mapped: 89.29

Strain: lineage4.1.1.3

Drug-resistance: Sensitive

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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
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.98
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
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 5150 c.-90G>C upstream_gene_variant 0.17
gyrB 5156 c.-84G>A upstream_gene_variant 0.15
gyrB 5761 p.Trp174Cys missense_variant 0.15
gyrB 5954 p.Glu239Lys missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8064 p.Gly255* stop_gained 0.14
gyrA 8174 c.873C>A synonymous_variant 0.17
gyrA 8275 p.Lys325Met missense_variant 0.18
gyrA 8791 p.Arg497Leu missense_variant 0.22
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620310 c.420C>T synonymous_variant 0.13
ccsA 620340 c.450C>G synonymous_variant 0.12
ccsA 620715 c.825C>T synonymous_variant 0.2
rpoB 759847 p.Ser14Thr missense_variant 0.11
rpoB 761045 p.Asn413Lys missense_variant 0.22
rpoB 761147 c.1341C>T synonymous_variant 0.17
rpoB 761150 c.1344A>T synonymous_variant 0.2
rpoB 761165 c.1359G>C synonymous_variant 0.18
rpoB 761168 c.1362C>G synonymous_variant 0.18
rpoB 761171 c.1365C>T synonymous_variant 0.18
rpoB 761178 c.1372_1374delTCAinsAGC synonymous_variant 0.18
rpoB 761189 c.1383T>C synonymous_variant 0.17
rpoB 761195 c.1389G>C synonymous_variant 0.2
rpoB 761198 c.1392G>C synonymous_variant 0.2
rpoB 761204 c.1398C>G synonymous_variant 0.2
rpoB 761537 c.1731C>A synonymous_variant 0.14
rpoB 761557 p.Ala584Gly missense_variant 0.11
rpoB 761565 p.Met587Leu missense_variant 0.11
rpoB 761570 c.1764T>C synonymous_variant 0.11
rpoB 761573 c.1767C>G synonymous_variant 0.11
rpoB 761579 c.1773G>C synonymous_variant 0.12
rpoC 762896 c.-474G>C upstream_gene_variant 0.22
rpoC 762932 c.-438G>C upstream_gene_variant 0.22
rpoC 762959 c.-411G>C upstream_gene_variant 0.25
rpoC 762962 c.-408C>T upstream_gene_variant 0.22
rpoC 763635 p.Arg89His missense_variant 0.2
rpoC 764540 c.1172_1176delTCACC frameshift_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766261 c.2892G>T synonymous_variant 0.15
rpoC 767137 c.3768G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776503 p.Glu660Gln missense_variant 0.2
mmpL5 778588 c.-108A>G upstream_gene_variant 0.13
mmpL5 778872 c.-392C>T upstream_gene_variant 0.15
mmpS5 778899 p.Gly3* stop_gained 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781495 c.-65G>A upstream_gene_variant 0.22
rpsL 781622 c.63C>T synonymous_variant 1.0
rpsL 781802 c.243G>C synonymous_variant 0.17
rpsL 781816 p.Arg86Leu missense_variant 0.21
fbiC 1302975 c.45C>A synonymous_variant 0.15
fbiC 1304764 p.Thr612Ala missense_variant 0.92
embR 1417029 p.Asp107Tyr missense_variant 0.18
embR 1417451 c.-104G>T upstream_gene_variant 0.17
embR 1417525 c.-178G>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471661 n.-185C>A upstream_gene_variant 0.14
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.38
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.29
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.22
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.67
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.5
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.5
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.6
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.5
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.5
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.5
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.5
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.5
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.43
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.43
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.43
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.43
rrl 1474832 n.1175A>T non_coding_transcript_exon_variant 0.43
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.4
rrl 1475081 n.1424C>T non_coding_transcript_exon_variant 0.33
rrl 1475396 n.1739C>A non_coding_transcript_exon_variant 0.33
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.33
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.38
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.38
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.45
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.45
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.36
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.4
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.44
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.44
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.38
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.33
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.4
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.18
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.4
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.57
rrl 1476470 n.2813C>G non_coding_transcript_exon_variant 0.29
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.25
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.33
fabG1 1673599 p.Gly54Trp missense_variant 0.2
rpsA 1833853 p.Lys104Asn missense_variant 0.15
rpsA 1833994 c.453G>C synonymous_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918716 c.777G>T synonymous_variant 0.17
tlyA 1918733 p.Ser265Asn missense_variant 0.14
ndh 2101936 c.1107G>T synonymous_variant 0.33
ndh 2102118 p.Leu309Met missense_variant 0.2
ndh 2102633 p.Gly137Asp missense_variant 0.25
katG 2154390 c.1722G>A synonymous_variant 0.33
katG 2154844 p.Val423Ala missense_variant 0.4
katG 2155942 p.Pro57Arg missense_variant 0.14
PPE35 2167691 c.2922C>A synonymous_variant 0.17
PPE35 2167820 c.2793G>T synonymous_variant 0.15
PPE35 2168506 p.Gly703Ser missense_variant 0.15
PPE35 2169430 p.Gly395Ser missense_variant 0.14
PPE35 2169488 c.1125G>A synonymous_variant 0.14
PPE35 2169605 p.Asn336Lys missense_variant 0.29
PPE35 2169616 p.Asn333Asp missense_variant 0.29
Rv1979c 2222443 p.Ala241Asp missense_variant 0.15
Rv1979c 2222507 p.Ser220Gly missense_variant 0.11
Rv1979c 2222598 c.567C>T synonymous_variant 0.29
Rv1979c 2222966 p.Thr67Ala missense_variant 0.15
Rv1979c 2223046 p.Ile40Asn missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289464 c.-223A>G upstream_gene_variant 0.15
pncA 2289636 c.-395A>C upstream_gene_variant 1.0
kasA 2518244 p.His44Asn missense_variant 0.18
kasA 2518404 p.Ser97Tyr missense_variant 0.15
eis 2714308 p.Pro342Gln missense_variant 0.22
ahpC 2725938 c.-255G>C upstream_gene_variant 1.0
ahpC 2726333 p.Trp47Cys missense_variant 0.18
pepQ 2859417 c.1002C>A synonymous_variant 0.15
ribD 2986852 p.Gly5Asp missense_variant 0.18
ribD 2987006 p.Asp56Glu missense_variant 0.14
ribD 2987144 p.Gln102His missense_variant 0.18
Rv2752c 3064631 p.Ala521Thr missense_variant 0.17
Rv2752c 3065734 p.Ala153Val missense_variant 0.22
Rv2752c 3065757 c.435C>T synonymous_variant 0.25
Rv2752c 3065762 p.Phe144Ile missense_variant 0.29
Rv2752c 3065942 p.Glu84* stop_gained 0.2
Rv2752c 3066227 c.-36C>T upstream_gene_variant 1.0
thyA 3074337 c.135C>A synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086826 p.Val3Leu missense_variant 0.29
ald 3087048 p.Pro77Thr missense_variant 0.13
ald 3087869 p.Leu350Phe missense_variant 0.15
fbiD 3338948 c.-170T>C upstream_gene_variant 0.11
fbiD 3339178 p.Ala21Thr missense_variant 1.0
fbiD 3339422 p.Val102Ala missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.92
fprA 3474179 p.Pro58His missense_variant 0.25
whiB7 3568524 c.156C>T synonymous_variant 0.13
whiB7 3568752 c.-73C>T upstream_gene_variant 0.18
Rv3236c 3612102 p.Ile339Val missense_variant 0.12
Rv3236c 3612360 p.Gly253Trp missense_variant 0.25
Rv3236c 3612397 c.720G>A synonymous_variant 0.2
fbiA 3641050 p.Gln170* stop_gained 0.22
fbiB 3642486 p.Arg318Gly missense_variant 0.11
alr 3840373 c.1048C>T synonymous_variant 0.14
rpoA 3877561 p.Asp316Ala missense_variant 0.29
rpoA 3877812 p.Ile232Met missense_variant 0.12
rpoA 3877866 c.642G>T synonymous_variant 0.15
rpoA 3878646 c.-139G>T upstream_gene_variant 0.5
ddn 3986744 c.-100C>T upstream_gene_variant 0.2
ddn 3986943 p.Gly34Trp missense_variant 0.17
ddn 3987131 c.288C>A synonymous_variant 0.2
clpC1 4038480 p.Leu742His missense_variant 0.17
clpC1 4039347 p.Arg453Leu missense_variant 0.2
clpC1 4039517 c.1188C>T synonymous_variant 0.18
clpC1 4040360 c.344delA frameshift_variant 0.15
clpC1 4040504 c.201C>A synonymous_variant 0.17
embC 4239941 p.Arg27Trp missense_variant 0.18
embC 4240810 p.Trp316* stop_gained 0.22
embC 4240837 c.975C>T synonymous_variant 0.22
embC 4241183 p.Thr441Ala missense_variant 0.11
embC 4241490 p.Ala543Glu missense_variant 0.17
embC 4241593 c.1731C>T synonymous_variant 0.15
embC 4241807 p.Pro649Ser missense_variant 0.18
embC 4241812 p.Trp650Cys missense_variant 0.17
embC 4242191 c.2329C>T synonymous_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243239 p.His3Asn missense_variant 0.18
embA 4243268 c.36C>A synonymous_variant 0.2
embA 4245998 p.Trp922Cys missense_variant 0.22
embB 4247435 c.922C>A synonymous_variant 0.17
embB 4248882 p.Pro790Arg missense_variant 0.2
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4266961 p.Arg626Trp missense_variant 0.18
aftB 4267087 p.Leu584Val missense_variant 0.13
aftB 4267382 c.1455A>T synonymous_variant 0.17
aftB 4267387 p.His484Tyr missense_variant 0.23
ubiA 4269020 p.Gly272Arg missense_variant 0.12
ethA 4326472 c.1002G>A synonymous_variant 0.29
ethR 4327033 c.-516G>A upstream_gene_variant 0.21
ethA 4327230 p.Leu82Ile missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0