TB-Profiler result

Run: ERR1023302
Summary

Run ID: ERR1023302

Sample name:

Date: 31-03-2023 09:16:45

Number of reads: 3929746

Percentage reads mapped: 87.07

Strain: lineage3;La3

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
La3 M.orygis None None 0.05
lineage3 East-African-Indian CAS RD750 0.97
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 761140 p.His445Leu missense_variant 0.86 rifampicin
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.14 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 6289 c.1050C>T synonymous_variant 0.13
gyrA 6319 c.-983G>C upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8225 c.924T>C synonymous_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 0.99
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760142 c.336C>G synonymous_variant 0.14
rpoB 760181 c.375T>C synonymous_variant 0.17
rpoB 760184 c.378A>G synonymous_variant 0.17
rpoB 760196 c.390C>G synonymous_variant 0.17
rpoB 760223 c.417T>C synonymous_variant 0.15
rpoB 760235 c.429T>C synonymous_variant 0.15
rpoB 760283 c.477G>C synonymous_variant 0.16
rpoB 760298 c.492G>C synonymous_variant 0.15
rpoB 760328 c.522G>C synonymous_variant 0.15
rpoB 760331 c.525G>C synonymous_variant 0.15
rpoB 760340 c.534G>T synonymous_variant 0.16
rpoB 760361 c.555T>C synonymous_variant 0.17
rpoB 760370 c.564C>G synonymous_variant 0.15
rpoB 760406 c.600G>C synonymous_variant 0.14
rpoB 760646 c.840C>G synonymous_variant 0.17
rpoB 760655 c.849A>G synonymous_variant 0.16
rpoB 760661 c.855A>C synonymous_variant 0.17
rpoB 760670 c.864G>C synonymous_variant 0.16
rpoB 760679 c.873A>G synonymous_variant 0.15
rpoB 761129 c.1323G>C synonymous_variant 0.15
rpoB 761132 c.1326G>T synonymous_variant 0.14
rpoB 761133 c.1327T>C synonymous_variant 0.15
rpoB 761165 c.1359G>C synonymous_variant 0.15
rpoB 761180 c.1374A>C synonymous_variant 0.14
rpoB 761189 c.1383T>C synonymous_variant 0.15
rpoB 761195 c.1389G>C synonymous_variant 0.15
rpoB 761207 c.1401C>T synonymous_variant 0.19
rpoB 761213 c.1407G>C synonymous_variant 0.19
rpoB 761219 c.1413G>C synonymous_variant 0.18
rpoB 761249 c.1443A>G synonymous_variant 0.15
rpoB 761255 c.1449T>G synonymous_variant 0.15
rpoB 761261 c.1455G>T synonymous_variant 0.16
rpoB 761306 c.1500C>G synonymous_variant 0.16
rpoB 761570 c.1764T>C synonymous_variant 0.16
rpoB 761573 c.1767C>G synonymous_variant 0.17
rpoB 761579 c.1773G>C synonymous_variant 0.18
rpoB 761588 c.1782C>T synonymous_variant 0.18
rpoB 761606 c.1800C>G synonymous_variant 0.17
rpoB 761612 c.1806G>C synonymous_variant 0.17
rpoB 761615 c.1809A>C synonymous_variant 0.16
rpoB 761645 c.1839C>G synonymous_variant 0.13
rpoB 761648 c.1842T>C synonymous_variant 0.13
rpoB 761948 c.2142G>C synonymous_variant 0.14
rpoB 762008 c.2202C>T synonymous_variant 0.14
rpoB 762206 c.2400C>G synonymous_variant 0.14
rpoB 762233 c.2427G>C synonymous_variant 0.15
rpoB 762254 c.2448T>G synonymous_variant 0.14
rpoB 762257 c.2451C>G synonymous_variant 0.14
rpoB 762369 c.2563T>C synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762467 c.-903C>T upstream_gene_variant 0.14
rpoC 762827 c.-543G>C upstream_gene_variant 0.14
rpoC 762857 c.-513C>G upstream_gene_variant 0.15
rpoC 762860 c.-510G>C upstream_gene_variant 0.15
rpoC 762863 c.-507T>C upstream_gene_variant 0.15
rpoC 762929 c.-441G>C upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763190 c.-180C>T upstream_gene_variant 0.13
rpoC 763441 c.72C>T synonymous_variant 0.18
rpoC 763444 c.75T>C synonymous_variant 0.18
rpoC 763456 c.87A>G synonymous_variant 0.18
rpoC 763486 c.117T>G synonymous_variant 0.16
rpoC 763492 c.123G>C synonymous_variant 0.15
rpoC 763528 c.159G>A synonymous_variant 0.16
rpoC 763546 c.177A>G synonymous_variant 0.18
rpoC 763570 c.201G>C synonymous_variant 0.18
rpoC 763573 c.204G>C synonymous_variant 0.2
rpoC 763594 c.225C>T synonymous_variant 0.2
rpoC 763603 c.234C>T synonymous_variant 0.22
rpoC 763636 c.267T>C synonymous_variant 0.18
rpoC 763657 c.288G>A synonymous_variant 0.19
rpoC 763660 c.291T>G synonymous_variant 0.18
rpoC 763675 c.306C>G synonymous_variant 0.17
rpoC 763765 c.396T>C synonymous_variant 0.14
rpoC 763774 c.405G>C synonymous_variant 0.14
rpoC 763835 p.Ala156Met missense_variant 0.14
rpoC 763853 p.Val162Ile missense_variant 0.15
rpoC 763858 c.489A>G synonymous_variant 0.15
rpoC 763861 c.492C>T synonymous_variant 0.15
rpoC 763945 c.576T>C synonymous_variant 0.13
rpoC 763951 c.582G>C synonymous_variant 0.13
rpoC 764020 c.651C>T synonymous_variant 0.15
rpoC 764024 c.655_657delTTGinsCTC synonymous_variant 0.15
rpoC 764032 p.Asp221Glu missense_variant 0.16
rpoC 764040 p.Ser224Thr missense_variant 0.15
rpoC 764044 c.675T>C synonymous_variant 0.15
rpoC 764059 c.690G>T synonymous_variant 0.14
rpoC 764181 p.Asp271Gly missense_variant 0.9
rpoC 765529 c.2160C>T synonymous_variant 0.17
rpoC 765541 c.2172C>G synonymous_variant 0.16
rpoC 765553 c.2184C>T synonymous_variant 0.17
rpoC 765556 c.2187G>C synonymous_variant 0.17
rpoC 765559 c.2190G>C synonymous_variant 0.16
rpoC 765580 c.2211G>C synonymous_variant 0.14
rpoC 765734 p.Leu789Ala missense_variant 1.0
rpoC 765826 c.2457T>C synonymous_variant 0.13
rpoC 765835 c.2466C>T synonymous_variant 0.16
rpoC 765883 c.2514C>G synonymous_variant 0.15
rpoC 765886 c.2517C>G synonymous_variant 0.15
rpoC 765892 c.2523T>C synonymous_variant 0.16
rpoC 765937 c.2568T>C synonymous_variant 0.15
rpoC 765967 c.2598C>T synonymous_variant 0.15
rpoC 765982 c.2613C>G synonymous_variant 0.15
rpoC 765994 c.2625A>T synonymous_variant 0.14
rpoC 766021 c.2652G>C synonymous_variant 0.15
rpoC 766027 c.2658G>C synonymous_variant 0.16
rpoC 766765 c.3396A>C synonymous_variant 0.15
rpoC 766774 c.3405T>C synonymous_variant 0.16
rpoC 766801 c.3432C>G synonymous_variant 0.14
rpoC 766804 c.3435A>G synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781703 c.144G>T synonymous_variant 0.14
rpsL 781715 c.156T>C synonymous_variant 0.16
rpsL 781728 c.169T>C synonymous_variant 0.17
rpsL 781736 c.177T>C synonymous_variant 0.16
rpsL 781742 c.183C>T synonymous_variant 0.18
rpsL 781748 c.189C>G synonymous_variant 0.17
rpsL 781754 c.195G>C synonymous_variant 0.17
rpsL 781760 c.201T>C synonymous_variant 0.14
rpsL 781772 c.213C>A synonymous_variant 0.13
rplC 800612 c.-197A>G upstream_gene_variant 0.14
rplC 800618 c.-191T>C upstream_gene_variant 0.14
rplC 800627 c.-182C>T upstream_gene_variant 0.13
rplC 800648 c.-161A>T upstream_gene_variant 0.19
rplC 800654 c.-155T>C upstream_gene_variant 0.18
rplC 800693 c.-116A>G upstream_gene_variant 0.15
rplC 800703 c.-106T>C upstream_gene_variant 0.18
rplC 800715 c.-94A>C upstream_gene_variant 0.16
rplC 800720 c.-89T>C upstream_gene_variant 0.15
rplC 800723 c.-86C>G upstream_gene_variant 0.16
rplC 800747 c.-62C>G upstream_gene_variant 0.15
fbiC 1304553 c.1623C>T synonymous_variant 0.13
fbiC 1304875 p.Ile649Val missense_variant 0.13
fbiC 1304893 p.Gly655Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.14
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.16
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.16
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.16
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.15
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.14
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.14
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.15
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.15
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.15
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.16
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.15
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.15
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.14
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.17
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.18
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.19
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.19
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.2
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.21
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.22
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.2
rrl 1475267 n.1610G>A non_coding_transcript_exon_variant 0.2
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.2
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.2
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.21
rrl 1475313 n.1656G>A non_coding_transcript_exon_variant 0.19
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.18
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.16
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.17
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.17
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.17
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.14
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.17
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.16
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.16
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.15
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.15
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.19
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.19
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.17
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.17
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.18
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.17
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.16
inhA 1674846 p.Ile215Met missense_variant 0.14
inhA 1674864 c.663C>T synonymous_variant 0.14
inhA 1674870 c.669T>C synonymous_variant 0.14
inhA 1674879 c.678T>C synonymous_variant 0.15
rpsA 1833940 c.399C>G synonymous_variant 0.17
rpsA 1833971 c.430C>T synonymous_variant 0.2
rpsA 1833979 c.438T>C synonymous_variant 0.17
rpsA 1834000 c.459G>C synonymous_variant 0.19
rpsA 1834021 c.480C>T synonymous_variant 0.18
rpsA 1834030 c.489C>G synonymous_variant 0.15
rpsA 1834396 c.855G>C synonymous_variant 0.16
rpsA 1834411 c.870T>C synonymous_variant 0.16
rpsA 1834417 c.876G>C synonymous_variant 0.16
rpsA 1834423 c.882G>C synonymous_variant 0.16
rpsA 1834435 c.894G>C synonymous_variant 0.17
rpsA 1834451 c.910T>C synonymous_variant 0.15
rpsA 1834609 c.1068T>C synonymous_variant 0.15
rpsA 1834633 c.1092A>G synonymous_variant 0.16
rpsA 1834639 c.1098T>C synonymous_variant 0.15
rpsA 1834654 p.Glu371Asp missense_variant 0.15
rpsA 1834684 c.1143C>T synonymous_variant 0.15
rpsA 1834690 c.1149T>C synonymous_variant 0.17
rpsA 1834732 c.1191T>C synonymous_variant 0.15
rpsA 1834733 p.Ala398Ser missense_variant 0.15
rpsA 1834738 c.1197A>G synonymous_variant 0.15
rpsA 1834765 p.Glu408Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518220 c.106C>T synonymous_variant 0.14
kasA 2518528 c.414C>G synonymous_variant 0.16
kasA 2518540 c.426T>C synonymous_variant 0.16
kasA 2518561 c.447T>C synonymous_variant 0.14
kasA 2518825 c.711T>C synonymous_variant 0.15
kasA 2518864 c.750G>C synonymous_variant 0.16
kasA 2518879 c.765A>G synonymous_variant 0.18
kasA 2518885 c.771T>C synonymous_variant 0.16
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
thyX 3067602 p.Arg115Gln missense_variant 0.13
thyX 3067611 p.Lys112Thr missense_variant 0.14
thyX 3067652 c.294T>C synonymous_variant 0.14
thyX 3067761 p.Arg62Gln missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3877587 c.921A>G synonymous_variant 0.16
rpoA 3877776 c.732T>C synonymous_variant 0.14
rpoA 3877782 c.726T>C synonymous_variant 0.15
rpoA 3877791 c.717C>G synonymous_variant 0.15
rpoA 3877818 c.690A>G synonymous_variant 0.17
rpoA 3877839 c.669G>C synonymous_variant 0.18
rpoA 3877848 c.660C>T synonymous_variant 0.19
rpoA 3877857 c.651G>A synonymous_variant 0.21
rpoA 3877866 c.642G>C synonymous_variant 0.21
rpoA 3877875 c.633T>G synonymous_variant 0.17
rpoA 3877878 c.630G>C synonymous_variant 0.17
rpoA 3877890 c.618C>T synonymous_variant 0.16
rpoA 3877896 c.612G>C synonymous_variant 0.15
rpoA 3877900 p.Ser203Asn missense_variant 0.14
rpoA 3877909 p.Asn200Ser missense_variant 0.14
rpoA 3878001 c.507A>G synonymous_variant 0.15
rpoA 3878022 c.486T>C synonymous_variant 0.18
rpoA 3878028 c.480G>C synonymous_variant 0.17
rpoA 3878031 c.477T>C synonymous_variant 0.16
rpoA 3878040 c.468T>C synonymous_variant 0.17
rpoA 3878055 c.453A>G synonymous_variant 0.17
rpoA 3878058 c.450G>T synonymous_variant 0.16
rpoA 3878061 c.447G>C synonymous_variant 0.16
rpoA 3878067 c.441C>G synonymous_variant 0.15
rpoA 3878070 c.438T>C synonymous_variant 0.15
rpoA 3878076 c.432C>T synonymous_variant 0.14
rpoA 3878337 c.171T>C synonymous_variant 0.14
rpoA 3878346 c.162T>C synonymous_variant 0.14
clpC1 4038640 p.Asp689Asn missense_variant 0.13
clpC1 4038812 c.1893T>C synonymous_variant 0.14
clpC1 4038845 c.1860G>C synonymous_variant 0.19
clpC1 4038860 c.1845G>C synonymous_variant 0.17
clpC1 4038878 c.1827A>G synonymous_variant 0.16
clpC1 4038905 c.1800A>G synonymous_variant 0.15
clpC1 4038908 c.1797C>G synonymous_variant 0.14
clpC1 4038914 c.1791G>C synonymous_variant 0.15
clpC1 4038923 c.1780_1782delCTAinsTTG synonymous_variant 0.14
clpC1 4039064 c.1641C>T synonymous_variant 0.16
clpC1 4039097 c.1608G>C synonymous_variant 0.15
clpC1 4039103 c.1602T>C synonymous_variant 0.14
clpC1 4039106 c.1599G>C synonymous_variant 0.14
clpC1 4039112 c.1593C>G synonymous_variant 0.14
clpC1 4039121 c.1584T>C synonymous_variant 0.14
clpC1 4039145 c.1560G>C synonymous_variant 0.14
clpC1 4039169 p.Glu512Asp missense_variant 0.16
clpC1 4039172 c.1533A>G synonymous_variant 0.16
clpC1 4039178 c.1527G>C synonymous_variant 0.17
clpC1 4039183 c.1522T>C synonymous_variant 0.16
clpC1 4039186 c.1519C>T synonymous_variant 0.15
clpC1 4039274 c.1431G>C synonymous_variant 0.15
clpC1 4039952 c.753T>C synonymous_variant 0.18
clpC1 4039979 c.726C>G synonymous_variant 0.15
clpC1 4039988 c.717C>G synonymous_variant 0.14
embC 4240828 c.966G>A synonymous_variant 0.15
embC 4240831 c.969T>G synonymous_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embA 4245137 c.1905T>C synonymous_variant 0.14
embA 4245146 c.1914G>A synonymous_variant 0.14
embA 4245149 c.1917C>G synonymous_variant 0.15
embA 4245153 p.Ile641Val missense_variant 0.15
embA 4245182 c.1950T>C synonymous_variant 0.15
embA 4245189 c.1957C>T synonymous_variant 0.17
embA 4245198 p.Leu656Ile missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0