TB-Profiler result

Run: ERR2514672
Summary

Run ID: ERR2514672

Sample name:

Date: 31-03-2023 20:29:34

Number of reads: 584476

Percentage reads mapped: 99.73

Strain: lineage4.3.3

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
lineage4.3 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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8921 c.1620C>A synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491022 c.240C>A synonymous_variant 0.11
fgd1 491256 p.Lys158Asn missense_variant 0.12
fgd1 491288 p.Gly169Val missense_variant 0.17
mshA 575291 c.-57G>T upstream_gene_variant 0.12
mshA 575543 p.Gly66Ser missense_variant 0.15
ccsA 620098 c.208C>A synonymous_variant 0.13
ccsA 620188 p.Leu100Met missense_variant 0.12
ccsA 620199 p.Gln103His missense_variant 0.11
ccsA 620267 p.Ala126Val missense_variant 0.15
rpoB 759759 c.-48T>C upstream_gene_variant 0.2
rpoB 760284 p.Phe160Leu missense_variant 0.13
rpoC 763670 p.Val101Ile missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.92
rpoC 765550 c.2181C>T synonymous_variant 0.12
rpoC 766790 p.Val1141Phe missense_variant 0.12
rpoC 767165 p.Arg1266Ser missense_variant 0.12
rpoC 767220 p.Thr1284Asn missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775911 p.Arg857Gln missense_variant 0.14
mmpL5 776343 c.2131_2137delCCGGACG frameshift_variant 0.12
mmpL5 778063 p.Gln140Lys missense_variant 0.2
mmpS5 778821 p.Arg29Gly missense_variant 0.18
mmpR5 779068 p.Phe27Val missense_variant 1.0
rpsL 781375 c.-185T>A upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781426 c.-134C>A upstream_gene_variant 0.22
rpsL 781875 p.Gly106Cys missense_variant 0.12
fbiC 1302894 c.-37T>A upstream_gene_variant 0.13
fbiC 1304102 p.Arg391Leu missense_variant 0.25
fbiC 1304133 c.1203G>T synonymous_variant 0.17
fbiC 1304139 c.1209G>T synonymous_variant 0.2
fbiC 1304593 p.Thr555Ala missense_variant 0.29
fbiC 1305498 c.2568C>T synonymous_variant 0.15
Rv1258c 1406967 p.Asp125Gly missense_variant 0.15
embR 1416562 c.786C>G synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472132 n.287A>G non_coding_transcript_exon_variant 0.29
rrs 1472153 n.308G>T non_coding_transcript_exon_variant 0.67
rrs 1473259 n.1414C>A non_coding_transcript_exon_variant 0.25
rrl 1476790 n.3133A>T non_coding_transcript_exon_variant 0.29
fabG1 1674076 c.642delC frameshift_variant 0.22
inhA 1674304 p.Gln35Lys missense_variant 0.14
inhA 1674592 p.Ala131Ser missense_variant 0.11
rpsA 1834930 c.1389A>G synonymous_variant 0.4
tlyA 1917858 c.-82G>T upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917981 c.42G>T synonymous_variant 0.33
tlyA 1918068 c.129C>A synonymous_variant 0.17
tlyA 1918176 c.237C>A synonymous_variant 0.15
katG 2154688 p.Thr475Ser missense_variant 0.2
katG 2155254 c.858C>A synonymous_variant 0.12
katG 2155415 p.Glu233Lys missense_variant 0.15
katG 2155703 p.Asp137Asn missense_variant 0.18
katG 2155713 c.399C>T synonymous_variant 0.15
katG 2156568 c.-457G>C upstream_gene_variant 0.15
PPE35 2168346 p.Val756Ala missense_variant 0.11
PPE35 2169529 p.Leu362Met missense_variant 0.2
PPE35 2170592 c.21G>T synonymous_variant 0.11
Rv1979c 2222210 p.Ala319Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289137 c.105G>A synonymous_variant 0.14
pncA 2289775 c.-534C>A upstream_gene_variant 0.15
pncA 2289991 c.-750G>A upstream_gene_variant 0.18
kasA 2518003 c.-112A>T upstream_gene_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714320 p.Ala338Val missense_variant 0.14
eis 2715059 p.Arg92Ser missense_variant 0.13
eis 2715069 c.264G>T synonymous_variant 0.13
eis 2715100 p.Pro78Gln missense_variant 0.12
eis 2715584 c.-252T>C upstream_gene_variant 0.22
ahpC 2726608 p.Asp139Gly missense_variant 0.15
folC 2746152 p.Gly483Cys missense_variant 0.17
folC 2746175 p.Ala475Glu missense_variant 0.15
folC 2746505 p.Thr365Lys missense_variant 0.11
folC 2747596 c.3G>T start_lost 0.14
pepQ 2860144 c.266_274delAGGCCGGCG disruptive_inframe_deletion 0.12
pepQ 2860157 p.Gly88Ser missense_variant 0.12
pepQ 2860162 p.Arg86Pro missense_variant 0.12
pepQ 2860307 p.Gly38Trp missense_variant 0.12
Rv2752c 3064827 c.1365C>T synonymous_variant 0.15
Rv2752c 3065213 p.Thr327Ala missense_variant 0.1
Rv2752c 3065530 p.Thr221Met missense_variant 0.22
Rv2752c 3065804 p.Glu130* stop_gained 0.12
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
Rv2752c 3066234 c.-43G>T upstream_gene_variant 0.2
Rv2752c 3066262 c.-71C>T upstream_gene_variant 0.17
Rv2752c 3067072 c.-881C>T upstream_gene_variant 0.17
thyX 3067978 c.-33C>A upstream_gene_variant 0.18
thyX 3068073 c.-128C>A upstream_gene_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
thyA 3074420 c.51dupC frameshift_variant 0.15
thyA 3074628 c.-157G>T upstream_gene_variant 0.14
ald 3086738 c.-81delG upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086930 c.111A>G synonymous_variant 0.2
fbiD 3339721 p.Gly202Trp missense_variant 0.22
Rv3083 3449403 c.900G>A synonymous_variant 0.13
Rv3083 3449479 p.Glu326Gln missense_variant 0.12
Rv3083 3449826 c.1323C>T synonymous_variant 0.12
Rv3083 3449945 p.Gly481Val missense_variant 0.12
fprA 3473822 c.-185C>T upstream_gene_variant 0.13
fprA 3473856 c.-151C>G upstream_gene_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474034 p.Gly10Ser missense_variant 0.22
fprA 3474394 p.Gly130Cys missense_variant 0.14
Rv3236c 3612198 p.Ala307Ser missense_variant 0.2
Rv3236c 3612439 c.678C>A synonymous_variant 0.12
fbiA 3640949 p.Trp136Leu missense_variant 0.18
fbiB 3641573 p.Glu13Asp missense_variant 0.15
fbiB 3642118 p.Ala195Asp missense_variant 0.2
fbiB 3642215 c.681G>T synonymous_variant 0.17
fbiB 3642264 p.Gly244Trp missense_variant 0.15
alr 3840821 c.600C>T synonymous_variant 0.13
rpoA 3878529 c.-22G>A upstream_gene_variant 0.17
rpoA 3878676 c.-169G>A upstream_gene_variant 0.5
rpoA 3878695 c.-188C>A upstream_gene_variant 0.18
rpoA 3878699 c.-192C>A upstream_gene_variant 0.18
ddn 3987070 p.Ala76Val missense_variant 0.4
ddn 3987247 p.Asp135Ala missense_variant 0.12
clpC1 4038235 p.Arg824Ser missense_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038453 p.Leu751Pro missense_variant 0.11
clpC1 4038842 c.1863G>T synonymous_variant 0.12
clpC1 4039072 p.Pro545Thr missense_variant 0.14
clpC1 4039523 p.Phe394Leu missense_variant 0.15
embC 4239680 c.-183C>T upstream_gene_variant 0.14
embC 4240250 p.Leu130Met missense_variant 0.11
embC 4240535 p.Ser225Gly missense_variant 0.12
embC 4241305 c.1443C>A synonymous_variant 0.12
embC 4241532 p.Ile557Thr missense_variant 0.11
embA 4242358 c.-875C>A upstream_gene_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243282 p.Ala17Asp missense_variant 0.18
embA 4244806 p.Leu525Gln missense_variant 0.15
embA 4245313 p.Ala694Val missense_variant 0.29
embA 4246090 p.Trp953Leu missense_variant 0.12
embB 4246543 c.30C>T synonymous_variant 0.17
embB 4248039 p.Arg509His missense_variant 0.13
embB 4248043 c.1530C>A synonymous_variant 0.14
embB 4248796 c.2283G>T synonymous_variant 0.15
embB 4249116 p.Pro868Gln missense_variant 0.12
aftB 4268680 p.Glu53* stop_gained 0.14
ubiA 4269933 c.-100C>A upstream_gene_variant 0.14
ethA 4326285 p.Leu397Met missense_variant 0.13
ethR 4327018 c.-531G>T upstream_gene_variant 0.12
ethR 4327712 p.Gly55Val missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408091 p.Pro38Thr missense_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 1.0