TB-Profiler result

Run: ERR11050182

Summary

Run ID: ERR11050182

Sample name:

Date: 02-04-2023 15:00:18

Number of reads: 373823

Percentage reads mapped: 99.47

Strain: lineage3

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
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 2154827 p.Pro429Ser missense_variant 0.12 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
gyrA 9565 p.Tyr755Phe missense_variant 0.22
gyrA 9589 p.Val763Gly missense_variant 0.33
gyrA 9652 p.Ile784Ser missense_variant 1.0
gyrA 9661 p.Ala787Gly missense_variant 0.67
fgd1 491223 c.441C>T synonymous_variant 0.22
fgd1 491316 c.534C>G synonymous_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575412 p.Glu22Ala missense_variant 0.33
mshA 575437 c.90A>C synonymous_variant 0.29
mshA 576606 p.Ala420Gly missense_variant 1.0
mshA 576618 p.His424Pro missense_variant 0.67
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761989 p.Ala728Val missense_variant 0.2
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763032 p.Ala1076Thr missense_variant 0.29
rpoC 766582 c.3213C>A synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776073 p.Val803Gly missense_variant 0.3
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776887 p.Asn532Asp missense_variant 0.12
mmpL5 777423 p.Leu353Gln missense_variant 0.25
mmpL5 777728 c.753T>A synonymous_variant 0.33
mmpL5 777883 p.Gly200Arg missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781600 p.Asp14Val missense_variant 0.67
rplC 800744 c.-65G>T upstream_gene_variant 0.18
fbiC 1303047 c.117G>A synonymous_variant 0.22
fbiC 1303960 p.Arg344Gly missense_variant 0.33
fbiC 1304103 c.1173G>A synonymous_variant 0.33
embR 1417059 p.Ala97Thr missense_variant 0.2
embR 1417322 p.Lys9Thr missense_variant 0.2
embR 1417429 c.-83delC upstream_gene_variant 0.15
atpE 1461104 c.60C>G synonymous_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472542 n.697A>T non_coding_transcript_exon_variant 0.4
rrl 1473988 n.331T>C non_coding_transcript_exon_variant 0.13
rrl 1475795 n.2138A>C non_coding_transcript_exon_variant 0.25
rrl 1476416 n.2759C>G non_coding_transcript_exon_variant 0.33
fabG1 1673553 p.Asp38Glu missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918151 p.Val71Gly missense_variant 1.0
ndh 2102038 c.1005C>T synonymous_variant 0.25
ndh 2103048 c.-6C>T upstream_gene_variant 0.2
ndh 2103230 c.-188T>G upstream_gene_variant 0.5
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168250 p.Gln788Arg missense_variant 0.15
PPE35 2169071 c.1542A>T synonymous_variant 0.29
PPE35 2169791 p.Asn274Lys missense_variant 0.17
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
eis 2715049 p.Gly95Asp missense_variant 0.33
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
pepQ 2859933 c.486C>G synonymous_variant 0.33
ribD 2986822 c.-17G>A upstream_gene_variant 1.0
Rv2752c 3064628 p.Asn522Tyr missense_variant 0.25
thyX 3067642 p.Ser102Thr missense_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087763 p.Asn315Thr missense_variant 0.15
Rv3083 3448433 c.-71C>G upstream_gene_variant 0.25
Rv3083 3449420 p.Phe306Tyr missense_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475215 c.1209C>G synonymous_variant 0.15
whiB7 3568577 p.Gly35Ser missense_variant 0.2
fbiA 3640583 p.Arg14Pro missense_variant 0.29
fbiB 3641824 p.Asn97Thr missense_variant 0.33
alr 3841473 c.-53G>A upstream_gene_variant 1.0
rpoA 3877626 c.882C>T synonymous_variant 0.29
rpoA 3877849 p.Gly220Asp missense_variant 0.29
rpoA 3877886 p.Leu208Met missense_variant 0.33
clpC1 4040235 p.Gly157Ala missense_variant 0.33
clpC1 4040550 p.Leu52Trp missense_variant 0.33
clpC1 4040581 p.Glu42Lys missense_variant 0.17
clpC1 4040725 c.-21A>G upstream_gene_variant 0.11
panD 4044208 p.Ser25* stop_gained 0.33
embC 4240963 c.1101G>T synonymous_variant 0.17
embC 4241679 p.Val606Gly missense_variant 0.33
embC 4241862 p.Glu667Ala missense_variant 0.14
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243817 p.Phe195Leu missense_variant 0.4
embA 4244989 p.Ala586Val missense_variant 0.22
embA 4244994 p.Thr588Ser missense_variant 0.2
embB 4248026 c.1515delC frameshift_variant 0.13
embB 4248131 p.Arg540Gly missense_variant 0.29
embB 4248328 c.1815G>C synonymous_variant 0.56
embB 4249036 c.2523G>A synonymous_variant 0.25
aftB 4267400 c.1437G>C synonymous_variant 0.33
aftB 4267940 c.897T>G synonymous_variant 0.5
aftB 4268440 p.Asp133His missense_variant 0.25
aftB 4268985 c.-149A>G upstream_gene_variant 0.18
ethA 4327482 c.-9C>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0