TB-Profiler result

Run: ERR2229141
Summary

Run ID: ERR2229141

Sample name:

Date: 31-03-2023 16:44:02

Number of reads: 292610

Percentage reads mapped: 83.27

Strain: lineage4

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
lineage4 Euro-American LAM;T;S;X;H None 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
embR 1416660 p.Arg230Trp missense_variant 0.22 ethambutol
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 9089 c.1788G>A synonymous_variant 0.25
fgd1 491383 p.Glu201* stop_gained 0.29
rpoC 763229 c.-141G>A upstream_gene_variant 0.15
rpoC 763397 p.Leu10Ile missense_variant 0.22
rpoC 764770 p.Gln467His missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777164 c.1317C>G synonymous_variant 0.14
mmpL5 778217 p.Asp88Glu missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781538 c.-22G>A upstream_gene_variant 0.14
fbiC 1302876 c.-55A>T upstream_gene_variant 0.15
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1407211 p.Ala44Ser missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473998 n.341A>T non_coding_transcript_exon_variant 0.18
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rpsA 1833521 c.-21T>A upstream_gene_variant 0.29
rpsA 1834390 c.849G>T synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153913 p.Asn733Lys missense_variant 0.4
PPE35 2167774 p.Gly947Cys missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 1.0
PPE35 2167967 c.2646A>C synonymous_variant 0.67
PPE35 2167973 c.2640A>G synonymous_variant 0.67
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168876 p.Phe579Leu missense_variant 0.29
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169287 c.1326T>C synonymous_variant 0.18
PPE35 2169587 c.1026G>A synonymous_variant 0.14
PPE35 2169598 p.Phe339Ile missense_variant 0.14
PPE35 2169879 p.Phe245Ser missense_variant 0.19
PPE35 2169882 p.Ser244Asn missense_variant 0.19
PPE35 2169890 c.723C>T synonymous_variant 0.21
PPE35 2169893 c.720C>A synonymous_variant 0.25
PPE35 2169910 p.Asn235Tyr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518282 c.168A>G synonymous_variant 0.2
kasA 2518726 c.612G>T synonymous_variant 0.4
kasA 2518739 p.Ala209Ser missense_variant 0.33
folC 2746220 p.Ala460Glu missense_variant 0.33
folC 2747306 p.Ser98Ile missense_variant 0.4
Rv2752c 3065027 p.Arg389Trp missense_variant 0.4
fbiA 3640476 c.-67C>T upstream_gene_variant 0.29
fbiA 3641281 p.Ile247Phe missense_variant 0.2
alr 3841015 p.Arg136Gly missense_variant 0.25
alr 3841018 c.403C>T synonymous_variant 0.25
alr 3841026 p.Val132Ala missense_variant 0.25
alr 3841546 c.-126C>A upstream_gene_variant 0.22
ddn 3987058 p.Arg72Gln missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.33
clpC1 4039829 p.Leu292Ile missense_variant 0.29
clpC1 4039850 c.855T>C synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242717 p.Leu952Pro missense_variant 0.5
embA 4245365 p.Phe711Leu missense_variant 0.22
embB 4247727 c.1217delG frameshift_variant 0.15
ethA 4326779 p.Thr232Ile missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407615 c.588G>A synonymous_variant 0.67
Rv3083 3448494 c.-9_*1408del transcript_ablation 1.0