TB-Profiler result

Run: ERR4820174

Summary

Run ID: ERR4820174

Sample name:

Date: 01-04-2023 16:31:42

Number of reads: 495284

Percentage reads mapped: 89.57

Strain:

Drug-resistance: Other


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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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.2.1.1 Indo-Oceanic NA RD239 1.0
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
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.75 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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7665 p.Asp122Asn missense_variant 0.2
gyrA 8390 c.1089C>A synonymous_variant 0.29
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9167 c.1866C>T synonymous_variant 1.0
gyrA 9260 c.1959G>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575738 p.Ala131Ser missense_variant 0.12
mshA 576713 p.Gly456Ser missense_variant 0.22
rpoB 760872 p.Glu356Lys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 765428 p.Gln687Lys missense_variant 0.14
rpoC 765908 p.Leu847Val missense_variant 0.33
rpoC 767300 p.Gly1311Cys missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775746 p.Met912Thr missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776187 p.Phe765Ser missense_variant 0.11
mmpL5 776639 c.1842C>A synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800833 c.27delC frameshift_variant 0.14
rplC 801275 p.Thr156Lys missense_variant 0.2
fbiC 1303750 c.820T>C synonymous_variant 0.18
fbiC 1304144 p.Trp405* stop_gained 0.13
Rv1258c 1406736 p.Thr202Asn missense_variant 0.12
embR 1416604 c.744C>T synonymous_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
atpE 1460853 c.-192T>G upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.2
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.2
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.2
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.36
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.36
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.59
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.59
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.64
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.64
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.64
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.64
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.83
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.83
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.17
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.83
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.83
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.67
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.67
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.67
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.62
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.4
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.38
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.38
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.25
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.25
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.45
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.43
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.43
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.43
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.4
rrl 1473817 n.160T>A non_coding_transcript_exon_variant 0.4
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.2
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.22
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.2
fabG1 1673417 c.-23C>T upstream_gene_variant 0.15
fabG1 1673818 p.Met127Val missense_variant 0.22
rpsA 1834170 p.Thr210Asn missense_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918173 c.234G>A synonymous_variant 0.12
tlyA 1918474 p.Pro179Thr missense_variant 0.29
ndh 2102592 c.449_450dupGC frameshift_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154941 p.Glu391* stop_gained 0.33
katG 2154990 c.1122C>A synonymous_variant 0.4
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168051 c.2562G>A synonymous_variant 0.29
PPE35 2168258 c.2355G>A synonymous_variant 0.22
PPE35 2168533 p.Val694Leu missense_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290129 c.-888C>A upstream_gene_variant 1.0
kasA 2517967 c.-148G>A upstream_gene_variant 0.2
kasA 2518124 p.Pro4Ala missense_variant 0.17
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518231 c.117C>T synonymous_variant 0.15
kasA 2519035 c.921C>T synonymous_variant 1.0
eis 2714829 c.504C>A synonymous_variant 0.29
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2747490 p.Arg37Cys missense_variant 0.12
pepQ 2860239 p.Tyr60* stop_gained 0.17
thyX 3067646 c.300C>G synonymous_variant 0.22
thyA 3073927 p.Ala182Val missense_variant 0.12
ald 3086699 c.-121C>A upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474724 p.Ala240Ser missense_variant 0.22
fprA 3475159 p.Asn385Asp missense_variant 1.0
fbiA 3640391 c.-152C>A upstream_gene_variant 0.17
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
rpoA 3877606 p.Leu301Pro missense_variant 0.22
ddn 3986843 c.-1C>A upstream_gene_variant 0.18
ddn 3986953 p.Leu37Pro missense_variant 0.18
ddn 3986982 p.Ala47Thr missense_variant 0.18
clpC1 4039014 p.Lys564Arg missense_variant 0.22
clpC1 4040241 p.Thr155Phe missense_variant 0.18
clpC1 4040249 p.Glu152Gly missense_variant 0.15
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044375 c.-94T>C upstream_gene_variant 0.2
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240688 p.Leu276Val missense_variant 0.14
embC 4240833 p.Phe324Ser missense_variant 0.15
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248515 p.Val668Ile missense_variant 1.0
aftB 4266991 p.Asp616Tyr missense_variant 0.22
aftB 4267221 p.Ala539Val missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327360 c.-189C>G upstream_gene_variant 1.0
ethR 4328138 p.Ala197Val missense_variant 0.2
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407913 p.Arg97His missense_variant 0.29
Rv3083 3448745 c.243_333delTNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN frameshift_variant 1.0