TB-Profiler result

Run: SRR15014712
Summary

Run ID: SRR15014712

Sample name:

Date: 03-04-2023 12:36:07

Number of reads: 2339781

Percentage reads mapped: 99.38

Strain: lineage1.2.2.2;lineage1.1.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.59
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.61
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.39
lineage1.2.2.2 Indo-Oceanic NA RD239 0.39
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 761095 p.Leu430Pro missense_variant 0.34 rifampicin
inhA 1674048 c.-154G>A upstream_gene_variant 0.57 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.31 isoniazid
katG 2155222 p.Gly297Val missense_variant 0.65 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.39
gyrB 6112 p.Met291Ile missense_variant 1.0
gyrB 6124 c.885C>T synonymous_variant 0.56
gyrA 7268 c.-34C>T upstream_gene_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7664 p.Asn121Lys missense_variant 0.38
gyrA 8435 c.1134C>G synonymous_variant 0.67
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575186 c.-162C>T upstream_gene_variant 0.36
mshA 576125 p.Gly260Arg missense_variant 0.48
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 765171 p.Pro601Leu missense_variant 0.49
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1407527 c.-187G>A upstream_gene_variant 0.44
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473123 n.1278A>G non_coding_transcript_exon_variant 0.68
rrl 1473660 n.3G>A non_coding_transcript_exon_variant 0.87
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.31
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.56
PPE35 2168742 p.Gly624Asp missense_variant 0.39
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 0.62
ald 3086788 c.-32T>C upstream_gene_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 3475159 p.Asn385Asp missense_variant 1.0
fbiB 3641811 c.277T>C synonymous_variant 0.54
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040719 c.-15A>G upstream_gene_variant 0.41
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 0.62
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267960 p.Val293Met missense_variant 0.35
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326148 c.1326G>T synonymous_variant 0.41
ethA 4326439 p.Asn345Lys missense_variant 0.34
whiB6 4338203 p.Arg107Cys missense_variant 0.3
whiB6 4338441 p.Tyr27* stop_gained 0.63
whiB6 4338449 p.Ala25Pro missense_variant 0.64
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 4407848 p.Ala119Thr missense_variant 0.45
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4408072 p.Leu44Arg missense_variant 0.39
gid 4408099 p.Leu35Pro missense_variant 0.59