TB-Profiler result

Run: ERR3077960
Summary

Run ID: ERR3077960

Sample name:

Date: 01-04-2023 00:12:44

Number of reads: 423686

Percentage reads mapped: 99.28

Strain: lineage4.2.2

Drug-resistance: MDR-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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
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
rpoB 761100 p.Gln432Glu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Met missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr 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 6375 p.Glu379Gly missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9155 c.1854C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9720 p.Gly807Cys missense_variant 0.12
fgd1 490936 p.Pro52Thr missense_variant 0.13
mshA 576077 c.730C>T synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.6
rpoB 759981 p.Ile59Phe missense_variant 0.15
rpoB 761248 p.Glu481Ala missense_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoB 762112 p.Asn769Thr missense_variant 1.0
rpoB 762977 p.Phe1057Leu missense_variant 0.2
rpoC 765358 p.Met663Ile missense_variant 0.17
rpoC 766966 p.Glu1199Asp missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775736 c.2745C>A synonymous_variant 0.2
mmpL5 775853 c.2628C>T synonymous_variant 0.15
mmpR5 779370 p.Asp127Glu missense_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781653 p.Gly32Ser missense_variant 0.2
rplC 801229 c.424dupC frameshift_variant 0.14
fbiC 1303041 c.112delA frameshift_variant 0.4
fbiC 1303517 p.Met196Lys missense_variant 0.2
fbiC 1304929 p.Thr667Ala missense_variant 0.17
Rv1258c 1406405 c.936G>A synonymous_variant 0.18
Rv1258c 1406432 p.Met303Ile missense_variant 0.13
embR 1416787 c.561C>A synonymous_variant 0.14
embR 1416971 p.Ala126Asp missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475259 n.1602T>G non_coding_transcript_exon_variant 1.0
rrl 1475337 n.1680C>T non_coding_transcript_exon_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101981 c.1062C>A synonymous_variant 0.12
ndh 2102196 p.Ser283Gly missense_variant 0.12
katG 2155478 p.Gly212Ser missense_variant 0.17
PPE35 2169895 p.Gly240Cys missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288911 p.Glu111* stop_gained 1.0
pncA 2288972 c.270C>A synonymous_variant 0.15
eis 2715470 c.-138G>T upstream_gene_variant 0.22
folC 2746270 c.1329C>A synonymous_variant 0.25
folC 2746388 p.Thr404Ile missense_variant 0.22
folC 2746684 c.915C>G synonymous_variant 0.14
folC 2746909 c.690C>A synonymous_variant 0.2
folC 2747485 p.Trp38* stop_gained 0.17
ribD 2986985 c.147G>A synonymous_variant 0.17
ribD 2987209 p.Gly124Ala missense_variant 0.15
Rv2752c 3065319 c.873C>T synonymous_variant 0.29
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
thyX 3067479 p.Asp156Val missense_variant 0.33
thyA 3074641 c.-170C>T upstream_gene_variant 0.4
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3475325 p.Pro440Arg missense_variant 0.18
Rv3236c 3612746 c.370dupG frameshift_variant 0.29
fbiB 3642801 p.Ala423Pro missense_variant 0.22
fbiB 3642805 p.Ile424Thr missense_variant 0.25
alr 3841348 p.Met25Leu missense_variant 0.18
rpoA 3877506 c.1001delG frameshift_variant 0.15
panD 4044374 c.-93G>A upstream_gene_variant 0.22
embC 4241983 c.2121G>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244830 p.Phe533Tyr missense_variant 0.12
embA 4244848 p.Gly539Val missense_variant 0.14
embB 4246022 c.-492C>A upstream_gene_variant 0.22
embA 4246314 p.Gly1028Cys missense_variant 0.22
embA 4246434 p.Gln1068Lys missense_variant 0.15
embB 4248028 c.1515C>T synonymous_variant 0.18
aftB 4267531 p.Ala436Ser missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0