TB-Profiler result

Run: ERR4831740
Summary

Run ID: ERR4831740

Sample name:

Date: 01-04-2023 21:05:36

Number of reads: 1466607

Percentage reads mapped: 93.41

Strain: lineage2.2.1

Drug-resistance: HR-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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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
rpsL 781687 p.Lys43Arg missense_variant 0.95 streptomycin
katG 2155163 p.Ile317Val missense_variant 0.14 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155740 c.371dupG frameshift_variant 0.17 isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619815 c.-76G>A upstream_gene_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620781 c.891C>G synonymous_variant 0.12
ccsA 620802 c.912C>G synonymous_variant 0.11
rpoB 762658 p.Ala951Asp missense_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
mmpL5 775611 p.Ser957* stop_gained 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304008 c.1078T>C synonymous_variant 0.12
fbiC 1305014 p.Thr695Met missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407154 p.Gly63Cys missense_variant 0.18
Rv1258c 1407197 c.144C>G synonymous_variant 0.11
embR 1416447 p.Tyr301His missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.11
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.13
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918298 p.Trp120Leu missense_variant 0.12
ndh 2102053 c.988_989delCC frameshift_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155024 p.Thr363Asn missense_variant 0.11
katG 2155177 p.Ala312Val missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170066 p.Ala183Thr missense_variant 0.18
PPE35 2170275 p.Asn113Ser missense_variant 0.1
Rv1979c 2222006 p.Ile387Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519143 c.1029G>T synonymous_variant 0.22
eis 2714526 c.805_806delAC frameshift_variant 1.0
eis 2715012 c.321C>A synonymous_variant 0.12
folC 2746915 c.684G>A synonymous_variant 0.15
folC 2747078 p.Glu174Gly missense_variant 0.11
Rv2752c 3065711 p.Gly161Ser missense_variant 0.96
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339434 p.Gly106Val missense_variant 0.12
Rv3083 3448358 c.-146G>T upstream_gene_variant 0.12
Rv3083 3448878 c.375C>G synonymous_variant 0.18
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641328 c.-207T>C upstream_gene_variant 0.11
fbiB 3642186 p.Arg218Gly missense_variant 0.11
rpoA 3877818 c.690A>G synonymous_variant 0.1
rpoA 3878646 c.-139G>T upstream_gene_variant 0.4
clpC1 4039022 c.1683A>G synonymous_variant 0.17
clpC1 4039046 c.1659C>G synonymous_variant 0.18
clpC1 4039067 c.1638G>C synonymous_variant 0.1
clpC1 4039070 c.1635G>C synonymous_variant 0.19
clpC1 4039077 p.Lys543Arg missense_variant 0.19
clpC1 4039079 c.1626C>G synonymous_variant 0.27
clpC1 4039085 c.1620A>G synonymous_variant 0.27
clpC1 4039091 c.1614G>T synonymous_variant 0.21
clpC1 4039097 c.1608G>T synonymous_variant 0.33
clpC1 4039103 c.1602T>C synonymous_variant 0.36
clpC1 4039106 c.1599G>C synonymous_variant 0.33
clpC1 4039121 c.1584T>C synonymous_variant 0.4
clpC1 4039142 c.1563A>G synonymous_variant 0.25
clpC1 4039145 c.1560G>C synonymous_variant 0.27
clpC1 4039445 p.Asp420Glu missense_variant 0.14
clpC1 4039466 c.1239T>C synonymous_variant 0.13
clpC1 4039469 c.1236T>C synonymous_variant 0.13
clpC1 4039472 c.1233G>C synonymous_variant 0.15
clpC1 4039478 c.1227G>C synonymous_variant 0.12
clpC1 4039481 c.1224T>C synonymous_variant 0.14
clpC1 4039487 c.1218G>C synonymous_variant 0.12
clpC1 4039571 c.1134G>T synonymous_variant 0.15
clpC1 4040248 p.Ala153Ser missense_variant 0.12
embC 4240476 p.Ala205Val missense_variant 0.12
embC 4241249 p.Arg463Ser missense_variant 0.12
embA 4242556 c.-677G>A upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242763 c.-470G>A upstream_gene_variant 0.13
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244544 p.Ala438Thr missense_variant 0.17
embA 4245669 p.Ala813Thr missense_variant 0.13
embA 4246026 c.2795dupC frameshift_variant 0.15
embB 4246644 p.Thr44Met missense_variant 0.13
embB 4246660 c.147C>T synonymous_variant 1.0
embB 4247825 p.Ala438Ser missense_variant 0.18
embB 4247852 p.Thr447Pro missense_variant 0.25
embB 4247902 c.1389G>T synonymous_variant 0.17
embB 4249023 p.Leu837Pro missense_variant 0.12
embB 4249733 p.Pro1074Ala missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267997 p.Leu280Phe missense_variant 0.17
aftB 4268552 p.Met95Ile missense_variant 0.13
whiB6 4338212 p.Tyr104His missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0