TB-Profiler result

Run: ERR2229722
Summary

Run ID: ERR2229722

Sample name:

Date: 31-03-2023 17:28:46

Number of reads: 835941

Percentage reads mapped: 99.26

Strain: lineage4.8

Drug-resistance: Sensitive

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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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
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 6703 c.-599G>A upstream_gene_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7449 p.Pro50Ala missense_variant 0.14
mshA 575954 p.Glu203* stop_gained 0.12
mshA 576113 c.766C>A synonymous_variant 0.12
ccsA 620407 p.Pro173Thr missense_variant 0.15
ccsA 620569 p.Gly227Arg missense_variant 0.17
rpoB 761152 p.Leu449Gln missense_variant 0.17
rpoB 762089 c.2283G>A synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776060 c.2421C>A synonymous_variant 0.14
mmpL5 776080 p.Ala801Ser missense_variant 0.14
mmpL5 776081 c.2400G>A synonymous_variant 0.14
mmpL5 776744 c.1737C>A synonymous_variant 0.13
mmpL5 776845 c.1633_1635delCAG conservative_inframe_deletion 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781553 c.-7C>T upstream_gene_variant 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
embR 1416571 c.777G>A synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473223 n.1378G>T non_coding_transcript_exon_variant 0.2
rrl 1474549 n.892G>A non_coding_transcript_exon_variant 0.2
rrl 1474755 n.1098G>T non_coding_transcript_exon_variant 0.18
rrl 1476009 n.2352G>T non_coding_transcript_exon_variant 0.4
fabG1 1673346 c.-94C>G upstream_gene_variant 0.15
fabG1 1673349 c.-91G>C upstream_gene_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.13
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
inhA 1674523 p.Phe108Ile missense_variant 0.12
rpsA 1834098 p.Ser186Cys missense_variant 0.15
rpsA 1834706 p.Asn389Tyr missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918517 p.Gly193Val missense_variant 0.11
ndh 2101788 p.Val419Leu missense_variant 0.12
ndh 2102356 c.687T>A synonymous_variant 0.15
ndh 2102966 p.Gly26Glu missense_variant 0.25
ndh 2102984 p.Ile20Thr missense_variant 0.29
katG 2154209 p.Gly635Cys missense_variant 0.12
katG 2155191 c.921A>C synonymous_variant 0.15
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168781 p.His611Arg missense_variant 0.11
PPE35 2169581 c.1032C>G synonymous_variant 0.12
PPE35 2169725 c.888T>C synonymous_variant 0.15
PPE35 2169890 c.723C>T synonymous_variant 0.14
PPE35 2169893 c.720C>A synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.32
PPE35 2170053 p.Thr187Ser missense_variant 0.32
Rv1979c 2222829 c.336T>C synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714209 p.Leu375Ser missense_variant 0.25
eis 2714740 c.592delG frameshift_variant 0.14
ahpC 2726616 p.Asn142Asp missense_variant 0.13
folC 2747571 p.Asp10Tyr missense_variant 0.12
pepQ 2860080 c.339G>T synonymous_variant 0.17
ribD 2986690 c.-149C>A upstream_gene_variant 0.14
ribD 2986965 p.Ala43Ser missense_variant 0.14
ribD 2987033 c.195C>A synonymous_variant 0.18
ribD 2987445 c.608delT frameshift_variant 0.15
thyA 3074144 p.Asp110Tyr missense_variant 0.17
thyA 3074622 c.-151C>T upstream_gene_variant 0.15
thyA 3074646 c.-175G>T upstream_gene_variant 0.2
fprA 3474185 c.180delC frameshift_variant 0.15
fbiA 3640723 p.Asp61Tyr missense_variant 0.12
ddn 3987073 p.Ala77Gly missense_variant 0.15
clpC1 4038616 p.Val697Ile missense_variant 0.2
embC 4241173 p.Phe437Leu missense_variant 0.17
embC 4241377 c.1516delG frameshift_variant 0.14
embC 4241563 c.1701C>A synonymous_variant 0.4
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244970 p.Leu580Met missense_variant 0.14
embB 4246548 p.Pro12Gln missense_variant 0.18
embB 4246555 c.42G>C synonymous_variant 0.18
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246582 c.69T>G synonymous_variant 0.22
embB 4247028 p.Leu172Arg missense_variant 0.15
embB 4249057 c.2545delA frameshift_variant 0.12
embB 4249615 c.3102C>T synonymous_variant 0.12
aftB 4268003 p.Leu278Phe missense_variant 0.2
whiB6 4338346 c.175dupC frameshift_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0