TB-Profiler result

Run: ERR3470647
Summary

Run ID: ERR3470647

Sample name:

Date: 01-04-2023 02:29:39

Number of reads: 2238500

Percentage reads mapped: 91.14

Strain: lineage3

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
lineage3 East-African-Indian CAS RD750 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
rpsL 781822 p.Lys88Met missense_variant 0.95 streptomycin
gid 4408100 c.102delG frameshift_variant 1.0 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
gyrA 6616 c.-686A>G upstream_gene_variant 0.13
gyrA 6622 c.-680C>T upstream_gene_variant 0.14
gyrA 6700 c.-602T>C upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9596 c.2295G>T synonymous_variant 0.93
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760223 c.417T>C synonymous_variant 0.14
rpoB 760340 c.534G>T synonymous_variant 0.14
rpoB 762233 c.2427G>C synonymous_variant 0.17
rpoB 762246 c.2440C>T synonymous_variant 0.17
rpoB 762254 c.2448T>G synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762989 c.-381G>C upstream_gene_variant 0.15
rpoC 762995 c.-375G>T upstream_gene_variant 0.16
rpoC 763013 c.-357C>G upstream_gene_variant 0.19
rpoC 763028 c.-342T>C upstream_gene_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763034 c.-336C>G upstream_gene_variant 0.18
rpoC 763040 c.-330C>G upstream_gene_variant 0.18
rpoC 763070 c.-300T>C upstream_gene_variant 0.16
rpoC 763085 c.-285C>G upstream_gene_variant 0.16
rpoC 763115 c.-255T>C upstream_gene_variant 0.15
rpoC 764112 p.Tyr248Phe missense_variant 0.14
rpoC 764116 c.747C>T synonymous_variant 0.14
rpoC 764131 c.762T>C synonymous_variant 0.14
rpoC 764140 c.771C>T synonymous_variant 0.17
rpoC 764181 p.Asp271Gly missense_variant 0.86
rpoC 764188 c.819A>G synonymous_variant 0.15
rpoC 764236 c.867G>A synonymous_variant 0.15
rpoC 764248 c.879C>G synonymous_variant 0.16
rpoC 764257 c.888G>C synonymous_variant 0.15
rpoC 764272 c.903G>C synonymous_variant 0.14
rpoC 764353 c.984G>C synonymous_variant 0.13
rpoC 764434 c.1065A>G synonymous_variant 0.14
rpoC 764489 c.1120C>T synonymous_variant 0.13
rpoC 767033 c.3664_3666delTCGinsAGC synonymous_variant 0.15
rpoC 767059 c.3690T>G synonymous_variant 0.15
rpoC 767062 c.3693C>A synonymous_variant 0.15
rpoC 767098 c.3729T>C synonymous_variant 0.19
rpoC 767111 c.3742C>T synonymous_variant 0.16
rpoC 767119 c.3750A>G synonymous_variant 0.16
rpoC 767134 c.3765C>A synonymous_variant 0.17
rpoC 767158 c.3789T>G synonymous_variant 0.15
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
fbiC 1304711 p.Ala594Asp missense_variant 0.12
fbiC 1304742 c.1812T>C synonymous_variant 0.14
fbiC 1304757 c.1827A>G synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472736 n.891G>A non_coding_transcript_exon_variant 0.96
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.13
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.14
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.14
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.14
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.15
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.15
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.15
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.15
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.17
inhA 1673985 c.-217C>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746810 p.Phe263Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878157 c.351C>G synonymous_variant 0.13
rpoA 3878163 c.345C>T synonymous_variant 0.14
rpoA 3878172 c.336G>C synonymous_variant 0.14
rpoA 3878226 c.282C>G synonymous_variant 0.17
rpoA 3878232 c.276G>C synonymous_variant 0.16
rpoA 3878247 c.261G>C synonymous_variant 0.18
rpoA 3878271 c.237T>C synonymous_variant 0.18
rpoA 3878284 p.Glu75Ala missense_variant 0.17
rpoA 3878292 c.216T>C synonymous_variant 0.18
rpoA 3878298 c.210A>G synonymous_variant 0.16
rpoA 3878304 c.204G>C synonymous_variant 0.2
rpoA 3878310 c.198G>C synonymous_variant 0.21
rpoA 3878313 c.195G>C synonymous_variant 0.18
rpoA 3878322 c.186A>G synonymous_variant 0.19
rpoA 3878331 c.177A>G synonymous_variant 0.19
rpoA 3878334 c.174T>C synonymous_variant 0.19
rpoA 3878337 c.171T>C synonymous_variant 0.21
rpoA 3878346 c.162T>C synonymous_variant 0.25
rpoA 3878364 c.144A>C synonymous_variant 0.27
rpoA 3878367 c.141C>G synonymous_variant 0.28
rpoA 3878376 c.132G>C synonymous_variant 0.23
rpoA 3878385 c.123C>G synonymous_variant 0.2
rpoA 3878388 c.120C>G synonymous_variant 0.2
rpoA 3878391 c.117T>C synonymous_variant 0.2
rpoA 3878415 c.93C>T synonymous_variant 0.18
rpoA 3878424 c.84G>C synonymous_variant 0.17
rpoA 3878436 c.72A>G synonymous_variant 0.17
rpoA 3878442 c.66G>C synonymous_variant 0.17
rpoA 3878478 c.30C>G synonymous_variant 0.13
rpoA 3878484 c.24C>A synonymous_variant 0.15
rpoA 3878490 c.18C>A synonymous_variant 0.14
rpoA 3878496 c.12A>T synonymous_variant 0.14
clpC1 4039121 c.1584T>C synonymous_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245198 p.Leu656Ile missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0