TB-Profiler result

Run: ERR4820442
Summary

Run ID: ERR4820442

Sample name:

Date: 01-04-2023 16:41:05

Number of reads: 619002

Percentage reads mapped: 99.63

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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
katG 2155168 p.Ser315Asn missense_variant 1.0 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 5815 c.576C>G synonymous_variant 0.14
gyrB 6372 p.Thr378Ser missense_variant 1.0
gyrA 6571 c.-731T>C upstream_gene_variant 0.17
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 576357 p.Ala337Val missense_variant 0.13
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760346 c.540C>T synonymous_variant 0.12
rpoB 760560 p.Met252Leu missense_variant 0.11
rpoB 761440 p.Asp545Val missense_variant 0.13
rpoB 761681 p.Glu625Asp missense_variant 0.29
rpoB 762155 c.2349C>A synonymous_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoB 762525 p.Val907Met missense_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766779 p.Glu1137Ala missense_variant 0.11
mmpL5 775606 p.Arg959Trp missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775728 p.Thr918Asn missense_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778183 p.Pro100Thr missense_variant 0.11
mmpL5 778504 c.-24G>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801406 p.Gly200Cys missense_variant 0.14
fbiC 1303928 p.Ala333Val missense_variant 1.0
Rv1258c 1407167 c.174C>A synonymous_variant 0.12
Rv1258c 1407335 c.6A>G synonymous_variant 0.22
embR 1416698 p.Leu217Pro missense_variant 0.22
embR 1417330 c.18A>C synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472060 n.215T>A non_coding_transcript_exon_variant 0.25
rrl 1476127 n.2470C>T non_coding_transcript_exon_variant 0.25
rrl 1476139 n.2482T>C non_coding_transcript_exon_variant 0.33
rrl 1476742 n.3085A>G non_coding_transcript_exon_variant 0.29
fabG1 1673163 c.-277G>C upstream_gene_variant 0.22
inhA 1674757 p.Ser186Pro missense_variant 0.1
inhA 1674912 c.711G>A synonymous_variant 0.22
rpsA 1834299 p.Gln253Leu missense_variant 0.14
rpsA 1834302 p.Val254Gly missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154097 p.Pro672Leu missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155424 p.Val230Met missense_variant 0.4
katG 2155765 p.His116Leu missense_variant 0.22
katG 2156260 c.-149C>A upstream_gene_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2170446 p.Ser56* stop_gained 0.33
Rv1979c 2222861 p.Ala102Ser missense_variant 0.17
Rv1979c 2222903 p.Arg88Cys missense_variant 0.17
Rv1979c 2222967 c.198G>A synonymous_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288724 p.Glu173Ala missense_variant 0.25
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289069 p.Phe58Cys missense_variant 0.13
pncA 2289365 c.-125delC upstream_gene_variant 1.0
kasA 2518211 p.Trp33Arg missense_variant 0.25
eis 2714673 c.660C>A synonymous_variant 0.14
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747544 p.Pro19Ser missense_variant 0.25
folC 2747734 c.-136C>T upstream_gene_variant 0.5
ribD 2986659 c.-180G>T upstream_gene_variant 0.11
Rv2752c 3065983 p.Arg70Gln missense_variant 0.18
thyA 3073796 p.Pro226Thr missense_variant 0.14
thyA 3074280 c.192C>T synonymous_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086863 p.Arg15Leu missense_variant 0.13
ald 3087157 p.Thr113Lys missense_variant 0.12
ald 3087303 p.Gly162Trp missense_variant 0.12
fbiD 3339434 p.Gly106Glu missense_variant 0.18
Rv3083 3448860 c.357G>T synonymous_variant 0.11
Rv3083 3448902 p.Cys133Trp missense_variant 0.12
Rv3083 3449004 c.501G>A synonymous_variant 0.15
Rv3083 3449264 p.Leu254Pro missense_variant 0.14
fprA 3473825 c.-182T>C upstream_gene_variant 0.12
fprA 3473854 c.-153G>A upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612750 p.Gly123Trp missense_variant 0.13
Rv3236c 3613223 c.-107C>T upstream_gene_variant 0.12
fbiA 3641155 p.Asp205Asn missense_variant 0.2
clpC1 4038211 c.2494C>T synonymous_variant 0.14
clpC1 4038347 c.2358G>A synonymous_variant 0.25
clpC1 4038660 c.2044delT frameshift_variant 0.12
clpC1 4039865 c.840T>C synonymous_variant 0.12
clpC1 4040150 c.555C>A synonymous_variant 0.2
clpC1 4040378 c.326delT frameshift_variant 0.25
panD 4043954 p.Ala110Thr missense_variant 1.0
panD 4044248 p.Arg12Ser missense_variant 0.22
embC 4242075 p.Arg738Gln missense_variant 1.0
embC 4242220 c.2358A>T synonymous_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242731 p.Trp957Arg missense_variant 0.11
embA 4243409 c.178delG frameshift_variant 0.15
embA 4243492 p.Gly87Val missense_variant 0.25
embA 4244284 p.Pro351Leu missense_variant 0.2
embA 4245625 p.Ser798* stop_gained 0.14
embA 4245641 p.Asn803Lys missense_variant 1.0
embB 4246809 c.299delG frameshift_variant 0.13
embB 4248277 c.1764G>T synonymous_variant 0.11
embB 4249521 p.Ala1003Val missense_variant 0.12
aftB 4267118 c.1719G>A synonymous_variant 0.15
aftB 4267526 c.1311C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407832 p.Val124Gly missense_variant 1.0