TB-Profiler result

Run: SRR4037647
Summary

Run ID: SRR4037647

Sample name:

Date: 04-04-2023 07:34:07

Number of reads: 1125897

Percentage reads mapped: 99.61

Strain: lineage4.4.1.1;lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.43
lineage4 Euro-American LAM;T;S;X;H None 0.48
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.54
lineage4.4 Euro-American S;T None 0.45
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.5
lineage4.4.1 Euro-American (S-type) S;T None 0.54
lineage4.4.1.1 Euro-American S;Orphans None 0.63
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 761095 p.Leu430Pro missense_variant 0.42 rifampicin
katG 2154730 c.1381delC frameshift_variant 0.12 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 7022 p.Leu595Met missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9138 p.Gln613Glu missense_variant 0.71
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490943 p.Ser54* stop_gained 0.17
fgd1 491742 c.960T>C synonymous_variant 0.38
mshA 575187 c.-161G>T upstream_gene_variant 0.17
mshA 575226 c.-122C>A upstream_gene_variant 0.12
mshA 575907 p.Ala187Val missense_variant 0.19
ccsA 620625 p.Ile245Met missense_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 0.48
rpoC 764529 p.Arg387His missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.54
mmpL5 776182 p.Asp767Asn missense_variant 0.4
mmpL5 777416 c.1065G>T synonymous_variant 0.58
mmpS5 779615 c.-710C>G upstream_gene_variant 0.56
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673363 c.-839G>A upstream_gene_variant 0.38
rpsA 1834177 c.636A>C synonymous_variant 0.5
rpsA 1834797 p.Ala419Val missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102222 p.Lys274Met missense_variant 0.11
ndh 2102990 p.Val18Ala missense_variant 0.53
katG 2154724 p.Arg463Leu missense_variant 0.18
katG 2155141 p.Thr324Asn missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 0.33
PPE35 2168479 p.Thr712Pro missense_variant 0.72
PPE35 2169320 p.Leu431Phe missense_variant 0.29
PPE35 2169840 p.Gly258Asp missense_variant 0.57
PPE35 2169866 c.747G>C synonymous_variant 0.26
PPE35 2170028 p.Met195Ile missense_variant 0.13
PPE35 2170032 p.Gly194Val missense_variant 0.12
PPE35 2170629 c.-17C>A upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715095 p.Ala80Ser missense_variant 0.14
pepQ 2859706 p.Val238Ala missense_variant 0.11
pepQ 2859961 p.Ala153Val missense_variant 0.2
Rv2752c 3066175 p.Pro6Arg missense_variant 0.45
thyX 3067356 p.Ala197Glu missense_variant 0.14
thyA 3074456 p.Asp6Tyr missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448608 c.105G>A synonymous_variant 0.74
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568779 c.-100T>C upstream_gene_variant 0.54
Rv3236c 3612665 p.Val151Ala missense_variant 0.3
Rv3236c 3612813 p.Thr102Ala missense_variant 0.38
fbiB 3641010 c.-525C>T upstream_gene_variant 0.13
fbiB 3642504 p.Asp324Tyr missense_variant 0.12
fbiB 3642521 c.987C>T synonymous_variant 0.12
clpC1 4039412 c.1293T>C synonymous_variant 0.14
panD 4044474 c.-193C>T upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.47
aftB 4267647 p.Asp397Gly missense_variant 0.18
ethR 4328195 p.Arg216His missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.56
gid 4407620 p.Tyr195His missense_variant 0.55
gid 4407927 p.Glu92Asp missense_variant 0.4