TB-Profiler result

Run: ERR2229105
Summary

Run ID: ERR2229105

Sample name:

Date: 31-03-2023 16:39:15

Number of reads: 572821

Percentage reads mapped: 99.35

Strain: lineage4.8

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
lineage4.8 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
katG 2154685 c.1426delG frameshift_variant 0.14 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 8923 p.Gly541Asp missense_variant 0.2
fgd1 490972 p.Arg64Ser missense_variant 0.12
mshA 576482 p.Val379Leu missense_variant 0.25
ccsA 620491 p.Ser201Thr missense_variant 0.12
rpoB 759896 c.90A>G synonymous_variant 0.13
rpoB 761358 p.Val518Ile missense_variant 0.14
rpoB 762149 c.2343G>T synonymous_variant 0.13
rpoC 763771 c.402C>T synonymous_variant 0.18
rpoC 765302 p.Glu645* stop_gained 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776816 c.1665T>A synonymous_variant 0.4
mmpL5 777391 p.Phe364Leu missense_variant 0.29
mmpL5 778272 p.Pro70Arg missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303179 c.249G>T synonymous_variant 0.23
fbiC 1303551 c.621G>T synonymous_variant 0.22
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406377 p.Gly322Ser missense_variant 0.15
Rv1258c 1407021 p.Ala107Asp missense_variant 0.13
embR 1416827 p.His174Arg missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473410 n.-248G>T upstream_gene_variant 0.17
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474781 n.1124C>A non_coding_transcript_exon_variant 0.13
rrl 1475938 n.2281C>T non_coding_transcript_exon_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.12
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.39
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103165 c.-123G>T upstream_gene_variant 0.12
katG 2154465 p.Cys549* stop_gained 0.13
katG 2154559 p.Ile518Asn missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.13
PPE35 2169351 p.Ala421Gly missense_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.28
PPE35 2169910 p.Asn235Tyr missense_variant 0.27
PPE35 2170048 p.Leu189Val missense_variant 0.36
PPE35 2170053 p.Thr187Ser missense_variant 0.42
PPE35 2170147 p.Ser156Ala missense_variant 0.16
Rv1979c 2222036 p.Leu377Met missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.18
kasA 2518882 c.768C>A synonymous_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.15
kasA 2519143 c.1029G>C synonymous_variant 0.17
ahpC 2726211 p.Gly7Cys missense_variant 0.12
ahpC 2726560 p.Gly123Val missense_variant 0.13
folC 2747122 c.477G>T synonymous_variant 0.22
folC 2747163 p.Gly146Cys missense_variant 0.33
pepQ 2859960 c.459G>T synonymous_variant 0.15
fbiD 3339516 c.399C>A synonymous_variant 0.18
fprA 3475240 p.Ala412Ser missense_variant 0.12
fprA 3475267 p.Ala421Ser missense_variant 0.15
whiB7 3568434 c.246G>T synonymous_variant 0.14
fbiB 3641674 c.142dupG frameshift_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.25
clpC1 4040831 c.-128delG upstream_gene_variant 0.11
panD 4044357 c.-77dupA upstream_gene_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243966 p.Arg245Pro missense_variant 0.14
embA 4244240 p.Trp336* stop_gained 0.22
embA 4244313 p.Val361Leu missense_variant 0.18
embA 4245280 p.Arg683Leu missense_variant 0.18
embB 4247573 p.Asp354Tyr missense_variant 0.15
aftB 4267020 p.Pro606Leu missense_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.13
whiB6 4338219 c.303C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448499 c.-4_*1408del transcript_ablation 1.0