TB-Profiler result

Run: ERR4831744
Summary

Run ID: ERR4831744

Sample name:

Date: 01-04-2023 21:05:46

Number of reads: 1550998

Percentage reads mapped: 98.78

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Trp missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.12 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 0.88 ethambutol
ethA 4327345 c.128delG frameshift_variant 0.1 ethionamide
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 7789 p.Pro163Arg missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490923 p.Gln47His missense_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575235 c.-113G>T upstream_gene_variant 0.12
mshA 575480 p.Arg45Ser missense_variant 0.13
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575921 p.Asp192Tyr missense_variant 0.15
mshA 575933 p.Pro196Thr missense_variant 0.13
mshA 576024 p.Ser226Trp missense_variant 0.13
mshA 576730 c.1383G>T synonymous_variant 0.33
mshA 576754 c.1407C>A synonymous_variant 0.11
ccsA 619795 c.-96C>T upstream_gene_variant 0.25
ccsA 619838 c.-53G>T upstream_gene_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620741 p.Thr284Lys missense_variant 0.13
rpoB 760903 p.His366Pro missense_variant 0.12
rpoB 760995 p.Arg397Gly missense_variant 0.12
rpoB 761196 c.1390C>T synonymous_variant 0.13
rpoB 761388 p.Asp528His missense_variant 0.2
rpoB 761399 c.1593C>T synonymous_variant 0.14
rpoB 761571 p.Pro589Ala missense_variant 0.1
rpoB 761701 p.Ala632Asp missense_variant 0.14
rpoB 762333 p.Gly843Arg missense_variant 0.11
rpoB 762522 p.Pro906Ala missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764010 p.Arg214His missense_variant 0.17
rpoC 764521 p.Asn384Lys missense_variant 0.13
rpoC 764545 c.1176C>G synonymous_variant 0.12
rpoC 765342 p.Pro658Leu missense_variant 0.14
rpoC 765347 p.Asp660His missense_variant 0.14
rpoC 765407 p.Gly680Ser missense_variant 0.13
rpoC 765625 c.2256C>A synonymous_variant 0.13
rpoC 765678 p.Arg770His missense_variant 0.15
rpoC 765731 p.Ala788Ser missense_variant 0.13
rpoC 766051 c.2682G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775644 p.Arg946Leu missense_variant 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776298 p.Ser728Ile missense_variant 0.11
mmpL5 777044 c.1437C>G synonymous_variant 0.1
mmpL5 777318 p.Arg388His missense_variant 0.25
mmpL5 777743 c.738C>G synonymous_variant 0.12
mmpL5 777907 p.Leu192Val missense_variant 0.14
mmpL5 778419 p.Arg21Gln missense_variant 0.22
mmpL5 779172 c.-692C>T upstream_gene_variant 0.22
mmpR5 779347 p.Val120Leu missense_variant 0.12
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801282 c.474G>C synonymous_variant 0.18
fbiC 1304038 p.Pro370Thr missense_variant 0.13
fbiC 1304117 p.Pro396His missense_variant 0.12
fbiC 1304231 p.Pro434Gln missense_variant 0.15
fbiC 1305060 c.2130C>T synonymous_variant 0.14
Rv1258c 1406750 c.591C>A synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407148 p.Ala65Ser missense_variant 0.2
embR 1416222 p.Phe376Leu missense_variant 0.11
embR 1416232 p.Cys372Gly missense_variant 0.11
embR 1416280 c.1068A>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.1
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.11
rrl 1473812 n.155G>A non_coding_transcript_exon_variant 0.12
rrl 1473814 n.157A>T non_coding_transcript_exon_variant 0.12
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.12
rrl 1473839 n.182G>A non_coding_transcript_exon_variant 0.11
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.12
rrl 1474477 n.820C>T non_coding_transcript_exon_variant 0.14
rrl 1474519 n.862G>A non_coding_transcript_exon_variant 0.14
rrl 1474561 n.904G>T non_coding_transcript_exon_variant 0.17
rrl 1475247 n.1590G>A non_coding_transcript_exon_variant 0.14
rrl 1475325 n.1668C>A non_coding_transcript_exon_variant 0.2
rrl 1476131 n.2474C>A non_coding_transcript_exon_variant 0.15
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.17
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.17
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.17
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.14
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476338 n.2685delG non_coding_transcript_exon_variant 0.14
rrl 1476576 n.2919C>G non_coding_transcript_exon_variant 0.17
inhA 1674062 c.-140C>A upstream_gene_variant 0.14
inhA 1674210 c.9A>C synonymous_variant 1.0
inhA 1674331 p.Leu44Met missense_variant 0.11
inhA 1674765 c.564C>T synonymous_variant 0.14
rpsA 1833959 p.Leu140Val missense_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918218 c.279C>T synonymous_variant 0.14
ndh 2102242 c.801G>T synonymous_variant 0.13
ndh 2102535 p.Leu170Ile missense_variant 0.12
katG 2153991 c.2121T>G synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155351 p.Arg254His missense_variant 0.14
katG 2155364 p.Glu250Lys missense_variant 0.17
katG 2155397 p.Pro239Thr missense_variant 0.13
katG 2156328 c.-217C>G upstream_gene_variant 0.17
katG 2156431 c.-320A>G upstream_gene_variant 0.12
katG 2156515 c.-404G>A upstream_gene_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170264 p.Leu117Val missense_variant 0.12
PPE35 2170402 p.Pro71Thr missense_variant 0.12
PPE35 2170516 p.Gly33Trp missense_variant 0.13
Rv1979c 2222062 p.Arg368Leu missense_variant 0.12
Rv1979c 2222417 p.Arg250Gly missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289423 c.-182A>G upstream_gene_variant 0.12
kasA 2518758 p.Ala215Asp missense_variant 0.2
kasA 2518976 p.Gly288Arg missense_variant 0.18
kasA 2519033 p.His307Asp missense_variant 0.22
kasA 2519197 c.1083G>T synonymous_variant 0.22
kasA 2519206 c.1092C>T synonymous_variant 0.22
eis 2715041 p.Arg98Gly missense_variant 0.25
eis 2715164 p.Glu57* stop_gained 0.12
eis 2715481 c.-149G>A upstream_gene_variant 0.13
eis 2715583 c.-251G>T upstream_gene_variant 0.29
ahpC 2726265 p.Lys25Gln missense_variant 0.19
ahpC 2726351 p.Trp53Cys missense_variant 0.14
folC 2746635 p.Asp322Asn missense_variant 1.0
folC 2747138 p.Val154Gly missense_variant 0.15
folC 2747466 p.Pro45Thr missense_variant 0.12
pepQ 2859721 p.Met233Thr missense_variant 0.12
pepQ 2859944 p.Ala159Ser missense_variant 0.12
Rv2752c 3064536 c.1656G>T synonymous_variant 0.11
Rv2752c 3064582 p.Val537Ala missense_variant 0.11
Rv2752c 3065060 p.Ala378Thr missense_variant 0.12
Rv2752c 3065304 c.888G>C synonymous_variant 0.12
Rv2752c 3065520 c.672G>T synonymous_variant 0.12
Rv2752c 3066107 p.Arg29Gly missense_variant 0.14
Rv2752c 3066287 c.-96G>C upstream_gene_variant 0.14
Rv2752c 3066329 c.-138C>A upstream_gene_variant 0.13
thyX 3067495 p.Glu151* stop_gained 0.2
thyX 3067538 c.408C>A synonymous_variant 0.18
thyX 3067907 c.39C>T synonymous_variant 0.17
thyX 3068018 c.-73G>A upstream_gene_variant 0.14
thyX 3068115 c.-170C>T upstream_gene_variant 0.12
thyX 3068135 c.-190G>C upstream_gene_variant 0.12
thyA 3073701 p.Ile257Met missense_variant 0.13
thyA 3074614 c.-143G>T upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087887 c.1068C>T synonymous_variant 0.14
fbiD 3339563 p.Ala149Val missense_variant 0.18
Rv3083 3449031 c.528C>G synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475256 p.Leu417Pro missense_variant 0.12
fprA 3475266 c.1260G>C synonymous_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640478 c.-65G>C upstream_gene_variant 0.2
fbiB 3641127 c.-408T>G upstream_gene_variant 0.14
fbiB 3641199 c.-336C>T upstream_gene_variant 0.22
fbiA 3641372 p.Gly277Val missense_variant 0.18
fbiB 3641625 p.Ala31Thr missense_variant 1.0
fbiB 3641678 c.144T>C synonymous_variant 0.11
fbiB 3641913 p.Ala127Ser missense_variant 0.25
fbiB 3642798 p.Gly422Ser missense_variant 0.13
alr 3840905 p.Phe172Leu missense_variant 0.12
alr 3841105 p.Thr106Pro missense_variant 0.11
alr 3841195 p.Arg76Cys missense_variant 0.12
ddn 3987055 p.Gly71Val missense_variant 0.12
ddn 3987058 p.Arg72Gln missense_variant 0.12
clpC1 4038449 c.2256C>G synonymous_variant 0.11
clpC1 4039105 p.Arg534Ser missense_variant 0.12
clpC1 4040244 p.Gly154Ala missense_variant 0.12
embA 4242286 c.-947C>T upstream_gene_variant 0.12
embC 4242372 p.Ala837Asp missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242802 c.-431G>T upstream_gene_variant 0.12
embA 4243388 c.156C>T synonymous_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243488 p.Gly86Ser missense_variant 0.14
embA 4243796 c.564C>A synonymous_variant 0.14
embA 4244347 p.Trp372* stop_gained 0.13
embA 4245603 p.Gly791Trp missense_variant 0.2
embA 4245733 p.Pro834Leu missense_variant 0.15
embA 4246462 p.Gly1077Asp missense_variant 0.17
embB 4246874 p.Gln121Lys missense_variant 0.12
embB 4247079 p.Phe189Ser missense_variant 0.14
embB 4247427 p.Gly305Ala missense_variant 0.11
embB 4247443 c.930C>A synonymous_variant 0.14
embB 4247885 p.Gly458Cys missense_variant 0.14
embB 4248594 p.Gly694Asp missense_variant 0.12
embB 4248868 c.2355G>A synonymous_variant 0.14
embB 4249132 c.2619G>A synonymous_variant 0.13
embB 4249140 p.Val876Gly missense_variant 0.14
embB 4249147 c.2634C>T synonymous_variant 0.15
embB 4249522 c.3009C>T synonymous_variant 0.15
embB 4249635 p.Asp1041Ala missense_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268201 c.636G>T synonymous_variant 0.14
whiB6 4338251 p.Ala91Pro missense_variant 0.17
whiB6 4338256 p.Ala89Glu missense_variant 0.2
whiB6 4338308 p.Ala72Thr missense_variant 0.17
whiB6 4338342 p.Trp60* stop_gained 0.17
whiB6 4338369 c.153C>G synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407532 p.Ala224Glu missense_variant 0.13
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0