TB-Profiler result

Run: ERR2229364

Summary

Run ID: ERR2229364

Sample name:

Date: 31-03-2023 17:05:57

Number of reads: 1167046

Percentage reads mapped: 98.84

Strain: lineage4.8

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
lineage4.8 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
embC 4240725 p.Gly288Val missense_variant 0.4 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.3
ccsA 620468 p.Ser193Asn missense_variant 0.12
ccsA 620554 p.Ala222Ser missense_variant 0.17
rpoB 760809 p.Thr335Ala missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776021 c.2460G>C synonymous_variant 0.11
mmpL5 777164 c.1317C>T synonymous_variant 0.17
mmpL5 777173 c.1308C>T synonymous_variant 0.17
mmpL5 777176 p.Glu435Asp missense_variant 0.18
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302913 c.-18C>G upstream_gene_variant 0.11
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304319 c.1389C>A synonymous_variant 0.12
Rv1258c 1407055 c.285delG frameshift_variant 0.12
embR 1417372 c.-25C>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474195 n.538A>G non_coding_transcript_exon_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.4
inhA 1674811 p.Gly204Ser missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102323 c.720C>G synonymous_variant 0.12
ndh 2103049 c.-7G>T upstream_gene_variant 0.15
ndh 2103157 c.-115G>T upstream_gene_variant 0.25
katG 2154639 c.1473C>G synonymous_variant 0.12
katG 2155002 c.1110G>C synonymous_variant 0.15
katG 2156446 c.-335C>T upstream_gene_variant 0.14
PPE35 2168053 p.Val854Met missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169602 c.1011C>A synonymous_variant 0.16
PPE35 2170048 p.Leu189Val missense_variant 0.59
PPE35 2170053 p.Thr187Ser missense_variant 0.62
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223325 c.-161G>T upstream_gene_variant 0.12
kasA 2519262 p.Asp383Gly missense_variant 0.12
eis 2714186 p.Leu383Ile missense_variant 0.18
eis 2714957 p.Tyr126His missense_variant 0.22
pepQ 2859753 c.666C>T synonymous_variant 0.13
Rv2752c 3064910 p.Ser428Gly missense_variant 0.17
Rv2752c 3065469 p.Asn241Lys missense_variant 0.22
Rv2752c 3065942 p.Glu84* stop_gained 0.12
thyA 3074312 p.Ser54Pro missense_variant 0.13
Rv3236c 3612412 c.705G>T synonymous_variant 0.25
Rv3236c 3612891 p.Glu76Lys missense_variant 0.13
fbiB 3642477 p.Asp315Tyr missense_variant 0.13
rpoA 3877888 p.Ala207Val missense_variant 0.15
clpC1 4039031 c.1674T>C synonymous_variant 0.14
clpC1 4040001 p.His235Pro missense_variant 0.12
embC 4239983 p.Ala41Ser missense_variant 0.12
embC 4240019 p.Asn53Asp missense_variant 0.11
embA 4242382 c.-851C>A upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245767 c.-747G>A upstream_gene_variant 0.13
embA 4246216 p.Glu995Gly missense_variant 0.29
embB 4246544 p.Thr11Pro missense_variant 0.62
embB 4246548 p.Pro12Gln missense_variant 0.6
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.43
embB 4246567 c.54G>T synonymous_variant 0.62
embB 4247059 c.546C>G synonymous_variant 0.13
embB 4247060 p.Pro183Ala missense_variant 0.13
embB 4247066 p.Ile185Val missense_variant 0.13
aftB 4268722 p.Arg39Cys missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0