TB-Profiler result

Run: SRR9940985
Summary

Run ID: SRR9940985

Sample name:

Date: 04-04-2023 23:02:12

Number of reads: 617745

Percentage reads mapped: 99.84

Strain: lineage4.9

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) T1 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
embR 1416212 p.Gln379Arg missense_variant 0.1 ethambutol
embC 4240841 p.Tyr327Asn missense_variant 0.17 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
gyrB 6828 p.Met530Thr missense_variant 0.12
gyrA 9263 c.1962C>A synonymous_variant 0.13
gyrA 9332 c.2031C>T synonymous_variant 0.22
fgd1 490931 p.His50Arg missense_variant 0.12
fgd1 491757 p.Gln325His missense_variant 0.12
mshA 575956 c.610delC frameshift_variant 0.17
rpoB 759768 c.-39G>T upstream_gene_variant 0.14
rpoB 760069 p.Ser88Tyr missense_variant 0.11
rpoB 760238 p.Gln144His missense_variant 0.11
rpoB 760325 c.519G>T synonymous_variant 0.11
rpoB 761152 p.Leu449Gln missense_variant 0.12
rpoB 761768 c.1962G>C synonymous_variant 0.12
rpoC 762428 c.-942C>A upstream_gene_variant 0.11
rpoB 762610 p.His935Arg missense_variant 0.15
rpoC 763376 p.Asp3Tyr missense_variant 0.12
rpoC 763471 c.102C>A synonymous_variant 0.15
rpoC 764850 p.His494Arg missense_variant 0.11
rpoC 765012 p.Ser548Ile missense_variant 0.14
rpoC 765742 p.Glu791Asp missense_variant 0.12
rpoC 767144 p.Pro1259Thr missense_variant 0.17
mmpL5 775721 c.2760C>T synonymous_variant 0.12
mmpL5 775765 p.Val906Phe missense_variant 0.12
mmpL5 777712 p.Gly257Trp missense_variant 0.17
mmpR5 778073 c.-917G>A upstream_gene_variant 0.12
rpsL 781449 c.-111G>T upstream_gene_variant 0.12
rplC 801320 p.Gly171Asp missense_variant 0.14
fbiC 1303016 p.Val29Gly missense_variant 0.27
fbiC 1303074 p.Met48Ile missense_variant 0.18
fbiC 1304355 c.1425G>T synonymous_variant 0.13
Rv1258c 1407290 c.51G>A synonymous_variant 0.15
embR 1416748 c.600A>G synonymous_variant 0.15
embR 1416842 p.Asp169Gly missense_variant 0.17
atpE 1460878 c.-167C>A upstream_gene_variant 0.14
atpE 1461136 p.Ala31Val missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472609 n.764G>T non_coding_transcript_exon_variant 0.11
rrl 1476106 n.2449A>G non_coding_transcript_exon_variant 0.12
rrl 1476170 n.2513C>T non_coding_transcript_exon_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.11
fabG1 1673359 c.-81T>C upstream_gene_variant 0.1
fabG1 1673361 c.-79C>G upstream_gene_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.29
inhA 1674594 c.393C>T synonymous_variant 0.17
rpsA 1833680 p.Asp47Tyr missense_variant 0.14
rpsA 1834049 p.Glu170* stop_gained 0.12
rpsA 1834805 p.Glu422* stop_gained 0.13
ndh 2102172 c.870dupC frameshift_variant 0.11
ndh 2102679 p.Gly122Cys missense_variant 0.12
katG 2155224 p.Met296Ile missense_variant 0.2
katG 2155803 c.309C>A synonymous_variant 0.14
PPE35 2168212 p.Ile801Val missense_variant 0.17
PPE35 2169022 p.Gly531Trp missense_variant 0.22
PPE35 2170048 p.Leu189Val missense_variant 0.75
PPE35 2170053 p.Thr187Ser missense_variant 0.73
PPE35 2170314 p.Val100Ala missense_variant 0.2
PPE35 2170598 c.15G>A synonymous_variant 1.0
Rv1979c 2221907 p.Val420Phe missense_variant 0.14
Rv1979c 2223051 p.Glu38Asp missense_variant 0.11
pncA 2289862 c.-621C>A upstream_gene_variant 0.14
kasA 2518702 c.588C>A synonymous_variant 0.13
folC 2746284 p.Ala439Pro missense_variant 0.17
folC 2746896 p.Gly235Trp missense_variant 0.14
pepQ 2860471 c.-53C>A upstream_gene_variant 0.14
pepQ 2860480 c.-62G>A upstream_gene_variant 0.13
Rv2752c 3065897 p.Asp99Asn missense_variant 0.14
Rv2752c 3066106 p.Arg29His missense_variant 0.12
ald 3087041 c.222C>A synonymous_variant 0.14
fprA 3475012 p.Asp336Tyr missense_variant 0.18
Rv3236c 3612381 p.Leu246Met missense_variant 0.12
fbiB 3641955 p.Gly141Cys missense_variant 0.12
fbiB 3642360 p.Val276Ile missense_variant 0.18
alr 3840596 p.Met275Ile missense_variant 0.11
rpoA 3877533 c.975C>A synonymous_variant 0.14
rpoA 3877804 p.Gly235Val missense_variant 0.25
clpC1 4039273 p.Glu478* stop_gained 0.12
panD 4044337 c.-56G>A upstream_gene_variant 0.3
embA 4242473 c.-760C>T upstream_gene_variant 0.15
embA 4242493 c.-740G>A upstream_gene_variant 0.12
embC 4242585 p.Ala908Asp missense_variant 0.13
embA 4243917 c.689delG frameshift_variant 0.17
embB 4245518 c.-996A>G upstream_gene_variant 0.18
embA 4245538 p.Pro769His missense_variant 0.22
embA 4245834 c.2603_2609delTGGTGGT frameshift_variant 0.18
embA 4245844 p.Val871Glu missense_variant 0.17
embA 4245846 p.Ser872Thr missense_variant 0.17
embA 4245848 c.2616_2617insACCACCA frameshift_variant 0.17
embA 4246185 p.Ala985Pro missense_variant 0.13
embB 4246973 p.His154Asn missense_variant 0.13
embB 4247384 p.His291Asn missense_variant 0.11
embB 4247902 c.1390delC frameshift_variant 0.12
embB 4249388 p.Asp959Tyr missense_variant 0.14
aftB 4266979 p.Gly620Trp missense_variant 0.22
aftB 4267933 p.Ala302Pro missense_variant 0.25
aftB 4267953 p.Ala295Glu missense_variant 0.18
aftB 4269321 c.-485G>A upstream_gene_variant 0.17
ethR 4327865 p.Gly106Glu missense_variant 0.13