TB-Profiler result

Run: ERR2245283
Summary

Run ID: ERR2245283

Sample name:

Date: 31-03-2023 17:37:14

Number of reads: 1172222

Percentage reads mapped: 99.42

Strain: lineage3.1.1

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 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili 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
rpsL 781822 p.Lys88Arg missense_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 6937 c.-365G>A upstream_gene_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7649 p.Phe116Leu missense_variant 0.12
gyrA 7946 c.645C>A synonymous_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491405 p.Met208Lys missense_variant 0.4
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.5
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763743 p.Leu125Gln missense_variant 0.13
rpoC 764605 c.1236G>T synonymous_variant 0.12
rpoC 766796 p.Arg1143Cys missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777259 p.Leu408Met missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303545 p.Lys205Asn missense_variant 0.11
Rv1258c 1407039 p.Val101Gly missense_variant 0.36
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674435 c.234G>T synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102676 c.363_366dupTGGC frameshift_variant 0.14
ndh 2102825 p.Arg73Leu missense_variant 0.12
katG 2154032 p.Val694Met missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169049 p.Ile522Phe missense_variant 0.17
PPE35 2169056 c.1557A>T synonymous_variant 0.18
PPE35 2169214 p.Ile467Val missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222500 p.Ala222Val missense_variant 0.15
Rv1979c 2222776 p.Ala130Asp missense_variant 0.25
Rv1979c 2223036 c.129A>G synonymous_variant 0.33
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
kasA 2518687 c.573C>T synonymous_variant 0.13
kasA 2518879 c.765A>G synonymous_variant 0.14
kasA 2518882 c.768C>A synonymous_variant 0.15
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
Rv2752c 3065523 p.His223Gln missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449372 p.Tyr290Phe missense_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612078 p.Ser347Ala missense_variant 0.18
Rv3236c 3612218 p.Val300Gly missense_variant 0.2
rpoA 3878490 c.18C>G synonymous_variant 0.55
clpC1 4038558 p.Ile716Asn missense_variant 0.12
embC 4240172 p.Val104Met missense_variant 1.0
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244355 p.Phe375Leu missense_variant 0.18
embA 4244358 p.Asn376Asp missense_variant 0.2
embA 4244976 p.Gly582Trp missense_variant 0.12
embA 4245438 p.Ala736Ser missense_variant 0.17
embB 4247023 c.510G>A synonymous_variant 0.13
aftB 4268619 p.Val73Gly missense_variant 0.25
ethR 4328110 p.Ala188Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408220 c.-18G>A upstream_gene_variant 0.13