TB-Profiler result

Run: SRR2100897
Summary

Run ID: SRR2100897

Sample name:

Date: 03-04-2023 23:21:30

Number of reads: 1214957

Percentage reads mapped: 99.37

Strain: lineage4.1.2.1

Drug-resistance: HR-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
lineage4.1 Euro-American T;X;H None 0.98
lineage4.1.2 Euro-American T;H None 0.96
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7471 p.Tyr57Ser missense_variant 0.11
gyrA 7495 p.Arg65His missense_variant 0.22
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491310 c.528C>T synonymous_variant 0.2
fgd1 491591 p.Lys270Met missense_variant 0.9
mshA 575627 p.Ala94Thr missense_variant 0.17
mshA 575679 p.Asn111Ser missense_variant 1.0
mshA 575687 p.Ala114Thr missense_variant 0.15
mshA 575765 p.Glu140* stop_gained 0.18
rpoB 760115 c.309C>T synonymous_variant 0.93
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766096 c.2727G>A synonymous_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778393 p.Thr30Ser missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 0.93
rplC 801226 p.Gly140Ser missense_variant 0.14
fbiC 1303953 c.1023C>T synonymous_variant 0.2
fbiC 1305211 p.Pro761Thr missense_variant 0.17
Rv1258c 1407102 p.Ala80Val missense_variant 0.14
embR 1416431 p.Ala306Val missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674952 p.Pro251Ala missense_variant 0.25
rpsA 1834868 p.Arg443Cys missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103196 c.-154G>T upstream_gene_variant 0.13
PPE35 2169320 p.Leu431Phe missense_variant 0.32
PPE35 2170462 p.Gly51Arg missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.93
eis 2714137 p.Ala399Val missense_variant 0.14
eis 2715008 p.Ala109Thr missense_variant 0.29
eis 2715521 c.-189C>T upstream_gene_variant 0.15
pepQ 2860148 p.Gly91Ser missense_variant 0.2
ribD 2987201 c.363C>G synonymous_variant 0.11
ribD 2987307 p.Ala157Pro missense_variant 0.25
thyX 3067228 p.Glu240Lys missense_variant 0.14
thyX 3067252 p.Val232Met missense_variant 0.17
thyX 3067508 p.Leu146Phe missense_variant 0.14
thyA 3073806 c.666C>G synonymous_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640721 p.Pro60Leu missense_variant 0.17
fbiB 3642486 p.Arg318Trp missense_variant 0.18
alr 3840944 c.477T>C synonymous_variant 0.12
ddn 3986695 c.-149G>A upstream_gene_variant 0.14
clpC1 4038857 c.1848C>A synonymous_variant 0.19
embC 4242425 p.Arg855Gly missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243476 c.244C>T synonymous_variant 1.0
embA 4244464 p.Ala411Asp missense_variant 0.13
embB 4247644 c.1131G>A synonymous_variant 0.14
ubiA 4269900 c.-67C>A upstream_gene_variant 0.18
ubiA 4269920 c.-87G>A upstream_gene_variant 0.21
ubiA 4270033 c.-200C>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0