TB-Profiler result

Run: ERR2229487
Summary

Run ID: ERR2229487

Sample name:

Date: 31-03-2023 17:16:08

Number of reads: 1084041

Percentage reads mapped: 99.25

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 0.99
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 7362 p.Glu21Gln missense_variant 1.0
rpoB 761030 c.1224G>A synonymous_variant 0.15
rpoB 761952 p.Ala716Ser missense_variant 0.18
rpoC 762557 c.-813G>C upstream_gene_variant 0.14
rpoB 762691 p.Pro962Leu missense_variant 0.15
rpoC 766751 p.Arg1128Gly missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776701 p.Ile594Val missense_variant 0.12
mmpS5 779638 c.-733C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781788 p.His77Asn missense_variant 0.13
fbiC 1303723 c.794_796delAGA disruptive_inframe_deletion 0.14
fbiC 1303739 c.809_810insTCT disruptive_inframe_insertion 0.13
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406184 p.Pro386His missense_variant 0.22
Rv1258c 1407235 c.104_105delTG frameshift_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.15
fabG1 1673346 c.-94C>G upstream_gene_variant 0.16
fabG1 1673349 c.-91G>C upstream_gene_variant 0.16
fabG1 1673357 c.-83G>A upstream_gene_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.28
fabG1 1674074 p.Gly212Val missense_variant 0.14
rpsA 1834066 p.Glu175Asp missense_variant 0.14
rpsA 1834523 p.Glu328* stop_gained 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102401 c.642T>C synonymous_variant 0.12
ndh 2102841 p.Ile68Phe missense_variant 0.2
ndh 2102875 c.168C>T synonymous_variant 0.22
katG 2155190 p.Thr308Ala missense_variant 0.17
PPE35 2167745 c.2868C>G synonymous_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.14
PPE35 2167967 c.2646A>C synonymous_variant 0.14
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168848 p.Val589Leu missense_variant 0.12
PPE35 2169269 c.1344A>G synonymous_variant 0.12
PPE35 2169278 c.1335T>C synonymous_variant 0.18
PPE35 2169281 c.1332T>G synonymous_variant 0.19
PPE35 2169287 c.1326T>C synonymous_variant 0.26
PPE35 2169293 c.1320T>C synonymous_variant 0.26
PPE35 2169308 c.1305C>T synonymous_variant 0.17
PPE35 2169902 p.Leu237Phe missense_variant 0.15
PPE35 2170048 p.Leu189Val missense_variant 0.43
PPE35 2170053 p.Thr187Ser missense_variant 0.45
PPE35 2170385 c.228G>T synonymous_variant 0.18
PPE35 2170392 p.Gly74Ala missense_variant 0.27
PPE35 2170400 c.213G>C synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289315 c.-74A>G upstream_gene_variant 0.29
kasA 2517967 c.-148G>C upstream_gene_variant 0.12
kasA 2518606 c.492G>C synonymous_variant 0.15
kasA 2518870 p.Glu252Asp missense_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.24
kasA 2518882 c.768C>A synonymous_variant 0.24
kasA 2518925 p.Thr271Ala missense_variant 0.12
kasA 2519313 p.Asn400Ile missense_variant 0.4
eis 2714747 p.Leu196Ile missense_variant 0.17
eis 2715221 p.Thr38Ala missense_variant 0.11
ahpC 2726080 c.-113G>T upstream_gene_variant 0.12
folC 2746278 p.Asp441Asn missense_variant 0.22
fbiD 3339741 c.624G>T synonymous_variant 0.17
fbiD 3339744 c.627A>C synonymous_variant 0.31
fprA 3475109 p.Ile368Asn missense_variant 0.13
fbiA 3640363 c.-180C>T upstream_gene_variant 0.12
fbiB 3642161 c.627G>T synonymous_variant 0.12
rpoA 3877595 p.Gly305Cys missense_variant 0.17
rpoA 3878527 c.-20C>T upstream_gene_variant 0.4
clpC1 4039018 p.Ser563Ala missense_variant 0.17
clpC1 4039022 c.1683A>G synonymous_variant 0.17
clpC1 4039031 c.1674T>C synonymous_variant 0.17
clpC1 4039669 p.Gln346Lys missense_variant 0.12
embA 4242379 c.-854G>A upstream_gene_variant 0.29
embA 4242473 c.-760C>T upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244864 c.1632G>A synonymous_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.36
embB 4246548 p.Pro12Gln missense_variant 0.57
embB 4246555 c.42G>C synonymous_variant 0.58
embB 4246556 p.Ala15Pro missense_variant 0.58
embB 4246563 p.Leu17Trp missense_variant 0.36
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4246747 p.Asp78Glu missense_variant 0.15
embB 4246877 p.Arg122Ser missense_variant 0.18
embB 4247028 p.Leu172Arg missense_variant 0.33
embB 4247990 p.Val493Leu missense_variant 0.13
aftB 4268793 p.Val15Ala missense_variant 0.2
ubiA 4269109 p.Gly242Asp missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0