TB-Profiler result

Run: ERR4822290
Summary

Run ID: ERR4822290

Sample name:

Date: 01-04-2023 17:45:12

Number of reads: 743373

Percentage reads mapped: 98.19

Strain: lineage4.2.1

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 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Leu missense_variant 1.0 pyrazinamide
embB 4248002 p.Gln497Lys missense_variant 1.0 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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7822 p.Leu174Gln missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491247 c.465C>T synonymous_variant 1.0
mshA 575480 p.Arg45Cys missense_variant 0.22
mshA 576108 p.Ala254Gly missense_variant 0.23
mshA 576431 p.Ala362Thr missense_variant 0.15
mshA 576720 c.1375delG frameshift_variant 0.22
rpoB 760306 p.Arg167His missense_variant 1.0
rpoB 762037 p.Ile744Thr missense_variant 0.11
rpoC 766340 p.Ile991Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303701 c.771C>T synonymous_variant 0.15
embR 1417083 p.Asp89Asn missense_variant 0.15
atpE 1461143 c.99C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.12
rrs 1472645 n.800G>A non_coding_transcript_exon_variant 0.11
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.15
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.1
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.12
rrs 1472924 n.1079G>T non_coding_transcript_exon_variant 0.12
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.11
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrl 1473934 n.277G>T non_coding_transcript_exon_variant 0.17
rrl 1473946 n.289A>G non_coding_transcript_exon_variant 0.18
rrl 1474003 n.346G>A non_coding_transcript_exon_variant 0.4
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.11
fabG1 1673346 c.-94C>G upstream_gene_variant 0.17
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.13
fabG1 1673361 c.-79C>G upstream_gene_variant 0.14
fabG1 1673380 c.-60C>G upstream_gene_variant 0.61
inhA 1673883 c.-319C>T upstream_gene_variant 0.12
inhA 1674780 c.580delA frameshift_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102367 p.Ala226Pro missense_variant 0.13
ndh 2102368 c.675C>T synonymous_variant 0.13
PPE35 2167814 c.2799C>T synonymous_variant 0.18
PPE35 2168003 p.His870Gln missense_variant 0.12
PPE35 2168145 p.Pro823Arg missense_variant 0.12
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.26
PPE35 2170053 p.Thr187Ser missense_variant 0.26
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518451 p.Gly113Ser missense_variant 0.14
eis 2715030 c.303C>T synonymous_variant 0.14
ahpC 2726142 c.-51G>A upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339364 p.Pro83Ala missense_variant 0.12
fprA 3473890 c.-117C>A upstream_gene_variant 0.14
fprA 3473959 c.-47delT upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474336 c.330C>A synonymous_variant 0.15
rpoA 3878535 c.-28G>T upstream_gene_variant 0.29
embC 4239860 c.-3G>T upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244511 p.Ile427Val missense_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.22
embB 4247138 c.627delG frameshift_variant 0.12
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4268497 p.Arg114Trp missense_variant 0.18
aftB 4268619 p.Val73Gly missense_variant 0.67
ethA 4327346 p.Gly43Val missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0