TB-Profiler result

Run: ERR4831792
Summary

Run ID: ERR4831792

Sample name:

Date: 01-04-2023 21:07:14

Number of reads: 415526

Percentage reads mapped: 89.96

Strain: lineage4;lineage2.2

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 0.96
lineage4 Euro-American LAM;T;S;X;H None 0.08
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.91
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.Ser450Leu missense_variant 0.92 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.6 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289069 p.Phe58Ser missense_variant 0.94 pyrazinamide
embB 4247429 p.Met306Val missense_variant 0.64 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 5605 c.366C>A synonymous_variant 0.29
gyrB 6519 p.Val427Glu missense_variant 0.18
gyrB 6845 p.Asp536Asn missense_variant 0.14
gyrA 7075 c.-227T>C upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8089 p.Ser263Tyr missense_variant 0.22
gyrA 8517 p.Ala406Thr missense_variant 0.15
gyrA 8958 p.Asp553His missense_variant 0.13
gyrA 9091 p.Ala597Asp missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491066 p.Cys95Phe missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576414 p.Gly356Val missense_variant 0.17
ccsA 620029 c.139C>T synonymous_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 0.93
rpoB 760181 c.375T>C synonymous_variant 0.12
rpoB 760193 c.387C>G synonymous_variant 0.1
rpoB 760663 p.Ala286Glu missense_variant 0.17
rpoB 760827 p.Arg341Ser missense_variant 0.33
rpoB 760962 p.Gly386Arg missense_variant 0.4
rpoB 762014 c.2208C>G synonymous_variant 0.12
rpoB 762038 c.2232C>T synonymous_variant 0.13
rpoB 762047 c.2241G>A synonymous_variant 0.17
rpoB 762053 c.2247T>C synonymous_variant 0.15
rpoB 762056 c.2250G>A synonymous_variant 0.15
rpoB 762065 c.2259T>G synonymous_variant 0.17
rpoC 762959 c.-411G>C upstream_gene_variant 0.29
rpoC 762962 c.-408C>T upstream_gene_variant 0.29
rpoC 762995 c.-375G>T upstream_gene_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763492 c.123G>C synonymous_variant 0.2
rpoC 763662 p.Ala98Asp missense_variant 0.33
rpoC 764913 p.Met515Lys missense_variant 0.14
rpoC 765631 c.2262C>T synonymous_variant 0.22
rpoC 766105 c.2736C>T synonymous_variant 0.15
rpoC 767080 c.3711G>C synonymous_variant 0.25
rpoC 767098 c.3729T>C synonymous_variant 0.22
rpoC 767104 c.3735C>G synonymous_variant 0.25
rpoC 767107 c.3738C>T synonymous_variant 0.25
rpoC 767320 c.3951G>A splice_region_variant&stop_retained_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775670 p.Phe937Leu missense_variant 0.18
mmpL5 775904 c.2577G>A synonymous_variant 0.12
mmpL5 775909 p.Leu858Phe missense_variant 0.12
mmpL5 775916 c.2565T>C synonymous_variant 0.12
mmpL5 775921 c.2560C>T synonymous_variant 0.12
mmpL5 775924 c.2557C>T synonymous_variant 0.12
mmpL5 775951 c.2530C>T synonymous_variant 0.2
mmpL5 775966 p.Ala839Ser missense_variant 0.25
mmpL5 776060 c.2421C>T synonymous_variant 0.5
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776984 c.1497C>T synonymous_variant 0.15
mmpL5 776995 p.Ser496Ala missense_variant 0.22
mmpL5 778303 p.Gln60Lys missense_variant 0.29
mmpL5 778908 c.-428G>T upstream_gene_variant 0.25
mmpL5 779376 c.-896C>A upstream_gene_variant 0.22
mmpS5 779524 c.-619C>A upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 0.71
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781616 c.57C>G synonymous_variant 0.67
rpsL 781626 p.Ala23Thr missense_variant 0.4
rpsL 781649 c.90T>C synonymous_variant 0.33
rplC 801124 p.Phe106Leu missense_variant 0.22
fbiC 1303349 c.420delC frameshift_variant 0.2
fbiC 1304586 c.1656C>T synonymous_variant 0.17
fbiC 1304868 c.1938G>T synonymous_variant 0.17
Rv1258c 1406642 c.699G>C synonymous_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406924 p.Leu139Phe missense_variant 0.18
Rv1258c 1407299 p.Phe14Leu missense_variant 0.18
Rv1258c 1407510 c.-170G>A upstream_gene_variant 0.33
embR 1417469 c.-122C>A upstream_gene_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472440 n.595G>A non_coding_transcript_exon_variant 0.4
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.38
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.12
rrs 1472950 n.1105C>T non_coding_transcript_exon_variant 0.15
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14
rrs 1473001 n.1156G>T non_coding_transcript_exon_variant 0.18
rrs 1473045 n.1200C>T non_coding_transcript_exon_variant 0.22
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.23
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.17
rrl 1473872 n.215A>G non_coding_transcript_exon_variant 0.33
rrl 1474344 n.687G>A non_coding_transcript_exon_variant 0.25
rrl 1474743 n.1086T>G non_coding_transcript_exon_variant 0.22
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.22
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.22
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.16
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.24
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.22
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.2
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.15
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.15
rrl 1475566 n.1909G>A non_coding_transcript_exon_variant 0.14
rrl 1476102 n.2445C>A non_coding_transcript_exon_variant 0.21
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.14
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.2
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.2
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.27
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.25
rrl 1476665 n.3008T>A non_coding_transcript_exon_variant 0.33
rrl 1476666 n.3009C>T non_coding_transcript_exon_variant 0.33
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.33
inhA 1674775 p.Gly192Cys missense_variant 0.15
rpsA 1833982 p.Phe147Leu missense_variant 0.22
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834431 p.Val297Gly missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918461 p.Asp174Glu missense_variant 0.15
tlyA 1918595 p.Gly219Val missense_variant 0.33
ndh 2101878 p.Gly389Cys missense_variant 0.15
ndh 2102850 p.Glu65* stop_gained 0.18
ndh 2103113 c.-71C>T upstream_gene_variant 0.2
katG 2154198 p.Tyr638* stop_gained 0.14
katG 2154724 p.Arg463Leu missense_variant 0.91
katG 2155040 p.Gly358Arg missense_variant 0.17
katG 2155562 p.Gly184Cys missense_variant 0.13
katG 2156487 c.-376G>A upstream_gene_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168051 c.2562G>T synonymous_variant 0.18
PPE35 2170286 c.327G>A synonymous_variant 0.29
Rv1979c 2221889 p.Val426Ile missense_variant 0.18
Rv1979c 2222729 p.Gly146Cys missense_variant 0.12
Rv1979c 2223154 p.Pro4Gln missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288894 c.348G>T synonymous_variant 0.15
pncA 2288941 p.Gly101Arg missense_variant 0.15
pncA 2289137 c.105G>C synonymous_variant 0.13
pncA 2290020 c.-780delC upstream_gene_variant 0.17
pncA 2290041 c.-800C>A upstream_gene_variant 0.17
pncA 2290153 c.-912C>T upstream_gene_variant 0.18
kasA 2518882 c.768C>G synonymous_variant 0.17
kasA 2518888 c.774C>T synonymous_variant 0.15
eis 2714526 c.805_806delAC frameshift_variant 0.43
eis 2715288 c.45G>T synonymous_variant 0.22
eis 2715540 c.-208C>A upstream_gene_variant 0.22
folC 2747462 p.Ser46Ile missense_variant 0.2
pepQ 2860306 p.Gly38Val missense_variant 0.2
pepQ 2860389 c.30G>T synonymous_variant 0.14
ribD 2986769 c.-70C>A upstream_gene_variant 0.29
Rv2752c 3064973 p.Ala407Thr missense_variant 0.17
Rv2752c 3065022 c.1170G>T synonymous_variant 0.13
Rv2752c 3065031 c.1161G>A synonymous_variant 0.14
Rv2752c 3065322 c.870C>T synonymous_variant 0.17
Rv2752c 3065711 p.Gly161Ser missense_variant 0.58
Rv2752c 3067074 c.-883C>A upstream_gene_variant 0.25
thyX 3067838 c.108C>T synonymous_variant 0.17
thyA 3073795 p.Pro226Leu missense_variant 0.18
thyA 3074330 p.Lys48Glu missense_variant 0.11
ald 3086687 c.-133G>T upstream_gene_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 0.88
fbiD 3339506 p.Ser130Leu missense_variant 0.25
fbiD 3339603 p.Phe162Leu missense_variant 0.29
Rv3083 3448870 p.Glu123* stop_gained 0.25
Rv3083 3449232 c.729C>A synonymous_variant 0.17
Rv3083 3449711 p.Gly403Val missense_variant 0.29
Rv3083 3449775 c.1272C>T synonymous_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.17
fprA 3474600 c.594G>T synonymous_variant 0.17
fprA 3475221 p.Gln405His missense_variant 0.18
whiB7 3568434 c.246G>T synonymous_variant 0.14
Rv3236c 3612571 c.546C>A synonymous_variant 0.5
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641833 p.Gly100Ala missense_variant 0.33
fbiB 3642377 c.843C>T synonymous_variant 0.17
fbiB 3642568 p.Pro345Leu missense_variant 0.27
alr 3840916 p.Pro169Ser missense_variant 0.25
alr 3841063 p.Phe120Ile missense_variant 0.25
rpoA 3877587 c.921A>G synonymous_variant 0.13
rpoA 3877593 c.915C>T synonymous_variant 0.13
rpoA 3878214 c.294C>T synonymous_variant 0.13
rpoA 3878343 c.165C>T synonymous_variant 0.25
rpoA 3878346 c.162T>C synonymous_variant 0.33
rpoA 3878364 c.144A>C synonymous_variant 0.29
rpoA 3878367 c.141C>G synonymous_variant 0.29
rpoA 3878370 c.138T>C synonymous_variant 0.33
rpoA 3878381 c.127C>T synonymous_variant 0.25
rpoA 3878391 c.117T>G synonymous_variant 0.25
rpoA 3878400 c.108T>C synonymous_variant 0.25
ddn 3986859 p.Pro6Ser missense_variant 0.33
ddn 3987077 c.234C>T synonymous_variant 0.2
clpC1 4038747 p.Arg653Leu missense_variant 0.25
clpC1 4040726 c.-22G>A upstream_gene_variant 0.17
panD 4044392 c.-111G>T upstream_gene_variant 0.29
embC 4240438 p.Asp192Glu missense_variant 0.33
embC 4240476 p.Ala205Asp missense_variant 0.25
embC 4240618 c.756C>T synonymous_variant 0.18
embC 4240720 p.Phe286Leu missense_variant 0.2
embC 4241030 c.1168C>T synonymous_variant 0.33
embC 4242212 p.Ala784Thr missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244082 p.Ala284Thr missense_variant 0.4
embA 4244754 p.Glu508* stop_gained 0.14
embB 4245623 c.-891G>A upstream_gene_variant 0.4
embB 4247443 c.930C>T synonymous_variant 0.15
embB 4248040 c.1527C>T synonymous_variant 0.15
embB 4249456 c.2943G>T synonymous_variant 0.33
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268904 c.-68C>T upstream_gene_variant 0.18
ubiA 4269388 p.Glu149Gly missense_variant 0.22
ubiA 4269818 p.Val6Met missense_variant 0.15
ethA 4326105 p.Leu457Met missense_variant 0.17
ethA 4326325 c.1149G>C synonymous_variant 0.14
ethA 4326809 p.Ala222Asp missense_variant 0.15
ethA 4327137 p.Glu113* stop_gained 0.12
ethA 4327227 p.Glu83* stop_gained 0.17
ethA 4328112 c.-639G>A upstream_gene_variant 0.17
whiB6 4338449 p.Ala25Ser missense_variant 0.15
whiB6 4338460 p.Met21Thr missense_variant 0.77
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.8
gid 4407891 p.Met104Ile missense_variant 0.14
gid 4407927 p.Glu92Asp missense_variant 0.93
gid 4408142 p.Arg21Trp missense_variant 0.22