TB-Profiler result

Run: ERR4831727

Summary

Run ID: ERR4831727

Sample name:

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

Number of reads: 493943

Percentage reads mapped: 94.58

Strain: lineage2.2.2

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
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 0.99
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 761139 p.His445Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
inhA 1674319 p.Gly40Trp missense_variant 0.33 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
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 5511 p.Ser91Phe missense_variant 0.17
gyrB 5620 c.381G>A synonymous_variant 0.17
gyrB 5643 p.Leu135Pro missense_variant 0.14
gyrB 6179 p.Gly314Ser missense_variant 0.14
gyrB 6530 p.Ser431Gly missense_variant 0.1
gyrB 6873 p.Leu545Ser missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7613 c.312G>A synonymous_variant 1.0
gyrA 8626 p.Arg442His missense_variant 0.13
gyrA 8648 p.Gln449His missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9806 p.Gln835His missense_variant 0.12
fgd1 490708 c.-75G>T upstream_gene_variant 0.18
fgd1 490747 c.-36C>T upstream_gene_variant 0.17
fgd1 490829 p.Ala16Glu missense_variant 0.29
fgd1 491213 p.Ser144Asn missense_variant 0.25
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575283 c.-65C>A upstream_gene_variant 0.67
mshA 576088 p.Phe247Leu missense_variant 0.14
mshA 576577 c.1230C>T synonymous_variant 0.18
ccsA 620279 p.Arg130Leu missense_variant 0.12
rpoB 759798 c.-9G>T upstream_gene_variant 0.14
rpoB 760010 c.204C>T synonymous_variant 0.14
rpoB 761579 c.1773G>A synonymous_variant 0.18
rpoB 761861 c.2055C>T synonymous_variant 0.4
rpoB 762182 p.Asp792Glu missense_variant 0.29
rpoB 762783 p.Asp993Asn missense_variant 0.22
rpoB 762946 p.Thr1047Ile missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763539 p.Asp57Gly missense_variant 0.18
rpoC 764018 p.Asp217Tyr missense_variant 0.33
rpoC 764180 p.Asp271Tyr missense_variant 0.15
rpoC 764347 c.978G>T synonymous_variant 0.14
rpoC 764984 p.Asp539Tyr missense_variant 0.13
rpoC 766663 c.3294G>T synonymous_variant 0.2
rpoC 766682 p.Val1105Phe missense_variant 0.18
rpoC 767253 p.Pro1295Leu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776418 p.Ser688* stop_gained 0.29
mmpL5 776853 p.Thr543Asn missense_variant 0.12
mmpL5 777010 p.Pro491Ser missense_variant 0.15
mmpL5 777306 p.Pro392His missense_variant 0.29
mmpL5 777354 p.Val376Ala missense_variant 0.5
mmpL5 777596 c.885G>T synonymous_variant 0.15
mmpL5 777676 c.805C>T synonymous_variant 0.29
mmpL5 778289 p.Met64Ile missense_variant 0.25
mmpL5 778348 p.Val45Ile missense_variant 0.18
mmpS5 778574 p.Ser111Phe missense_variant 0.17
mmpR5 779128 p.Asp47Tyr missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781857 p.Gly100Cys missense_variant 0.22
rplC 801446 p.Lys213Ile missense_variant 0.12
fbiC 1302970 p.Ser14Gly missense_variant 0.14
fbiC 1303078 p.Ala50Thr missense_variant 0.22
fbiC 1303308 c.379_381delGAG conservative_inframe_deletion 0.2
fbiC 1303427 p.Gly166Asp missense_variant 0.2
fbiC 1303535 p.Ser202* stop_gained 0.17
fbiC 1304444 p.Ala505Val missense_variant 0.25
fbiC 1304493 p.Asp521Glu missense_variant 0.22
Rv1258c 1406145 p.Ala399Val missense_variant 1.0
Rv1258c 1406211 p.His377Arg missense_variant 0.17
Rv1258c 1406869 p.Pro158Ser missense_variant 0.18
Rv1258c 1406956 p.Pro129Ser missense_variant 0.18
embR 1416434 p.Ala305Val missense_variant 0.14
embR 1416708 p.Ala214Thr missense_variant 0.14
embR 1416775 c.573C>T synonymous_variant 0.18
embR 1417044 p.Arg102Trp missense_variant 0.29
embR 1417169 p.Trp60Leu missense_variant 0.17
embR 1417295 p.Pro18Leu missense_variant 0.18
atpE 1461243 p.Asn67Asp missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471833 n.-13G>T upstream_gene_variant 0.15
rrs 1472276 n.431A>G non_coding_transcript_exon_variant 0.2
rrs 1472374 n.529T>C non_coding_transcript_exon_variant 0.11
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.13
rrs 1472766 n.921G>C non_coding_transcript_exon_variant 0.14
rrs 1473261 n.1416G>C non_coding_transcript_exon_variant 0.14
rrl 1474342 n.685G>C non_coding_transcript_exon_variant 0.4
rrl 1474974 n.1317G>T non_coding_transcript_exon_variant 0.22
rrl 1475315 n.1658A>G non_coding_transcript_exon_variant 0.14
rrl 1475535 n.1878G>T non_coding_transcript_exon_variant 0.18
rrl 1476125 n.2468G>T non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.17
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.15
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.17
rrl 1476528 n.2871A>G non_coding_transcript_exon_variant 0.17
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.17
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.22
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.22
rrl 1476668 n.3011C>A non_coding_transcript_exon_variant 0.15
inhA 1673796 c.-406G>T upstream_gene_variant 0.18
inhA 1674353 p.Thr51Ile missense_variant 0.17
inhA 1674377 p.Pro59Gln missense_variant 0.18
rpsA 1833529 c.-13G>T upstream_gene_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834521 p.Ala327Asp missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918231 p.Glu98Lys missense_variant 0.2
ndh 2102556 p.Asp163Asn missense_variant 0.14
ndh 2102944 c.99C>T synonymous_variant 0.14
ndh 2103009 p.Pro12Thr missense_variant 0.15
ndh 2103220 c.-178C>A upstream_gene_variant 0.12
katG 2154034 p.Arg693His missense_variant 0.17
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154750 p.Glu454Asp missense_variant 0.17
katG 2155375 p.Val246Ala missense_variant 0.33
katG 2155611 p.Phe167Leu missense_variant 0.2
katG 2156091 c.21C>A synonymous_variant 0.18
katG 2156470 c.-359C>A upstream_gene_variant 0.13
katG 2156476 c.-365G>A upstream_gene_variant 0.13
PPE35 2167877 p.Ser912Arg missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168065 p.Thr850Ala missense_variant 0.2
PPE35 2169628 p.Ile329Val missense_variant 0.11
PPE35 2169769 p.Ala282Thr missense_variant 0.25
PPE35 2169969 p.Gly215Val missense_variant 0.14
PPE35 2169992 c.621C>A synonymous_variant 0.14
Rv1979c 2222728 p.Gly146Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288758 p.Gly162Ser missense_variant 0.18
pncA 2288765 c.477G>A synonymous_variant 0.15
pncA 2289175 p.Gly23Ser missense_variant 0.2
pncA 2289565 c.-324G>A upstream_gene_variant 0.17
pncA 2289961 c.-720C>A upstream_gene_variant 0.17
kasA 2518411 c.297C>T synonymous_variant 0.4
kasA 2518956 p.Ala281Glu missense_variant 0.15
kasA 2519213 p.Ile367Phe missense_variant 1.0
eis 2714427 c.906G>A synonymous_variant 0.18
eis 2714438 p.Met299Val missense_variant 0.13
eis 2714709 c.624C>T synonymous_variant 0.18
eis 2714816 p.Gly173Ser missense_variant 0.22
eis 2714935 p.Pro133Leu missense_variant 0.22
eis 2714967 c.366G>A synonymous_variant 0.25
eis 2714983 p.Ala117Glu missense_variant 0.25
eis 2715392 c.-60G>T upstream_gene_variant 0.15
eis 2715568 c.-236G>A upstream_gene_variant 0.17
ahpC 2726293 p.Tyr34Cys missense_variant 0.13
ahpC 2726553 p.Ala121Thr missense_variant 0.14
ahpC 2726571 p.Ala127Thr missense_variant 0.15
folC 2746411 c.1188G>A synonymous_variant 0.5
folC 2747251 p.Ser116Arg missense_variant 0.15
folC 2747352 p.Asp83Tyr missense_variant 0.2
pepQ 2859732 p.Tyr229* stop_gained 0.15
pepQ 2860074 p.Glu115Asp missense_variant 0.15
pepQ 2860287 c.132G>T synonymous_variant 0.12
ribD 2986868 c.30T>C synonymous_variant 0.12
ribD 2987213 c.375C>A synonymous_variant 0.2
ribD 2987533 p.Gly232Glu missense_variant 0.17
Rv2752c 3065231 p.Gly321Trp missense_variant 0.14
Rv2752c 3065507 p.Ala229Ser missense_variant 0.17
Rv2752c 3066173 p.Pro7Thr missense_variant 0.17
Rv2752c 3066232 c.-41T>C upstream_gene_variant 0.11
Rv2752c 3066288 c.-97G>A upstream_gene_variant 0.15
thyA 3073890 p.Leu194Phe missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087024 c.206delA frameshift_variant 0.29
ald 3087110 c.291G>A synonymous_variant 0.18
ald 3087189 p.Asp124Tyr missense_variant 0.14
fbiD 3339199 p.Pro28Thr missense_variant 0.67
fbiD 3339646 p.Glu177Lys missense_variant 0.5
Rv3083 3448819 p.Thr106Ser missense_variant 0.15
Rv3083 3449253 c.750C>A synonymous_variant 0.14
Rv3083 3449924 p.Leu474Pro missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474024 c.18C>T synonymous_variant 0.2
fprA 3474169 p.Pro55Ser missense_variant 0.2
fprA 3474610 p.Pro202Thr missense_variant 0.29
fprA 3474903 c.897C>T synonymous_variant 0.14
fprA 3475376 c.1370G>A splice_region_variant&stop_retained_variant 0.22
whiB7 3568670 c.10C>T synonymous_variant 0.17
whiB7 3568737 c.-58C>A upstream_gene_variant 0.25
Rv3236c 3612545 p.Ala191Asp missense_variant 0.18
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613100 p.Ala6Val missense_variant 0.15
fbiA 3640981 p.Asp147Asn missense_variant 0.14
fbiA 3641472 p.Met310Ile missense_variant 0.25
fbiB 3641523 c.-12G>C upstream_gene_variant 0.13
fbiB 3641543 c.9C>A synonymous_variant 0.18
fbiB 3642621 p.Ala363Ser missense_variant 0.13
fbiB 3642635 p.Asp367Glu missense_variant 0.15
alr 3840654 p.Ala256Val missense_variant 0.12
alr 3840798 p.Asn208Ser missense_variant 0.1
rpoA 3877805 p.Gly235Trp missense_variant 0.14
rpoA 3878241 p.Glu89Asp missense_variant 0.11
rpoA 3878418 c.90C>T synonymous_variant 0.17
clpC1 4038338 c.2367C>A synonymous_variant 0.18
clpC1 4038728 c.1977C>T synonymous_variant 0.14
clpC1 4038851 c.1854G>A synonymous_variant 0.29
clpC1 4038863 c.1842G>T synonymous_variant 0.29
clpC1 4039204 p.Glu501Lys missense_variant 0.15
clpC1 4039697 c.1008C>T synonymous_variant 0.2
clpC1 4039820 c.885T>C synonymous_variant 0.14
clpC1 4040014 p.Gln231* stop_gained 0.15
clpC1 4040539 p.Leu56Met missense_variant 0.13
panD 4043917 p.Ala122Glu missense_variant 0.12
embC 4239921 p.Arg20Leu missense_variant 0.12
embC 4239951 p.Arg30Gln missense_variant 0.13
embC 4240680 p.Leu273Pro missense_variant 0.25
embC 4241549 p.Gly563Arg missense_variant 0.18
embC 4241605 c.1743C>T synonymous_variant 0.18
embC 4241644 c.1782G>A synonymous_variant 0.17
embC 4241692 c.1830C>T synonymous_variant 0.22
embC 4241744 p.Phe628Leu missense_variant 0.17
embC 4241999 p.Trp713Arg missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242869 p.Val1003Ile missense_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243526 c.294G>A synonymous_variant 0.15
embA 4243557 p.Ala109Ser missense_variant 0.25
embA 4243716 p.Leu162Met missense_variant 0.29
embA 4244007 p.Ala259Thr missense_variant 0.29
embB 4245827 c.-687C>T upstream_gene_variant 0.29
embB 4247131 c.618C>A synonymous_variant 0.29
embB 4247171 p.Leu220Val missense_variant 0.22
embB 4247667 p.Trp385Leu missense_variant 0.25
embB 4248795 p.Ala761Gly missense_variant 0.13
embB 4249312 c.2799C>A synonymous_variant 0.22
embB 4249424 c.2911C>T synonymous_variant 0.17
aftB 4267073 c.1764C>A synonymous_variant 0.18
aftB 4267222 p.Ala539Ser missense_variant 0.13
aftB 4267494 p.Gly448Val missense_variant 0.12
aftB 4267591 p.Gln416* stop_gained 0.2
aftB 4267593 p.Ala415Asp missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269046 p.Ala263Val missense_variant 0.2
ubiA 4269068 p.Thr256Ala missense_variant 0.2
aftB 4269666 c.-830G>T upstream_gene_variant 0.18
aftB 4269737 c.-901C>T upstream_gene_variant 0.11
ethA 4326013 c.1461G>T synonymous_variant 0.15
ethA 4326039 p.Arg479Trp missense_variant 0.12
ethA 4326130 c.1344G>A synonymous_variant 1.0
ethA 4327058 p.Gly139Asp missense_variant 0.85
ethA 4327149 p.Trp109Arg missense_variant 0.12
ethR 4327841 p.Asp98Gly missense_variant 0.14
ethR 4328110 p.Ala188Ser missense_variant 0.13
ethR 4328147 p.Leu200Pro missense_variant 0.11
ethA 4328445 c.-972A>G upstream_gene_variant 0.29
whiB6 4338208 p.Pro105Gln missense_variant 0.17
whiB6 4338358 p.Ala55Asp missense_variant 0.17
whiB6 4338577 c.-56G>A upstream_gene_variant 0.13
whiB6 4338579 c.-58C>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407704 p.Ala167Ser missense_variant 0.33
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408062 c.141G>A synonymous_variant 0.2
gid 4408235 c.-33T>G upstream_gene_variant 0.17
gid 4408264 c.-62C>T upstream_gene_variant 0.18
gid 4408379 c.-177C>A upstream_gene_variant 0.4