TB-Profiler result

Run: ERR2229389
Summary

Run ID: ERR2229389

Sample name:

Date: 31-03-2023 17:09:03

Number of reads: 518851

Percentage reads mapped: 98.77

Strain: lineage4

Drug-resistance: RR-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
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 761105 p.Phe433Leu missense_variant 0.13 rifampicin
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 5053 c.-187C>T upstream_gene_variant 0.12
gyrB 5349 p.Thr37Asn missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7959 p.Met220Val missense_variant 0.33
mshA 576108 p.Ala254Gly missense_variant 0.2
mshA 576111 p.Ala255Gly missense_variant 0.25
rpoB 759653 c.-154C>A upstream_gene_variant 0.22
rpoB 759810 p.Ala2Thr missense_variant 0.17
rpoC 766424 p.Gly1019Ser missense_variant 0.25
rpoC 766690 c.3321G>A synonymous_variant 0.2
rpoC 767126 p.Ile1253Phe missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800838 p.Lys10Asn missense_variant 0.29
fbiC 1303625 p.Gly232Val missense_variant 0.4
fbiC 1303652 p.Arg241Leu missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303952 p.Asp341Gly missense_variant 0.17
fbiC 1304441 p.Arg504Leu missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473142 n.1297G>T non_coding_transcript_exon_variant 0.29
rrs 1473289 n.1444T>C non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474139 n.482C>A non_coding_transcript_exon_variant 0.4
rrl 1476139 n.2482T>C non_coding_transcript_exon_variant 0.33
fabG1 1673300 c.-140G>A upstream_gene_variant 0.17
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
inhA 1674340 p.Ile47Phe missense_variant 0.4
rpsA 1833985 c.444G>A synonymous_variant 0.15
rpsA 1834955 p.Ala472Ser missense_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918165 p.Ala76Ser missense_variant 0.27
ndh 2101777 c.1266C>A synonymous_variant 0.5
ndh 2102986 c.57C>A synonymous_variant 0.29
katG 2154292 p.Glu607Val missense_variant 0.2
katG 2156280 c.-169T>A upstream_gene_variant 0.25
PPE35 2167745 p.Thr956Arg missense_variant 0.29
PPE35 2167865 c.2748G>C synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.17
PPE35 2168215 p.Thr800Ala missense_variant 0.18
PPE35 2168220 p.Ala798Glu missense_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169383 c.1230C>A synonymous_variant 0.13
PPE35 2169457 p.His386Asp missense_variant 0.14
PPE35 2169462 p.Val384Pro missense_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.69
PPE35 2170147 p.Ser156Ala missense_variant 0.2
PPE35 2170159 p.Ala152Ser missense_variant 0.16
PPE35 2170169 c.444A>G synonymous_variant 0.11
PPE35 2170175 c.438G>C synonymous_variant 0.11
PPE35 2170178 c.435T>C synonymous_variant 0.11
PPE35 2170392 p.Gly74Ala missense_variant 0.12
PPE35 2170400 c.213G>C synonymous_variant 0.14
Rv1979c 2221889 p.Val426Phe missense_variant 0.14
Rv1979c 2223191 c.-27G>A upstream_gene_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288834 p.Asp136Glu missense_variant 0.14
pncA 2288914 p.Asp110Tyr missense_variant 0.17
kasA 2518606 c.492G>C synonymous_variant 0.75
kasA 2518609 p.Met165Ile missense_variant 0.75
kasA 2518956 p.Ala281Glu missense_variant 0.33
folC 2746411 c.1188G>T synonymous_variant 0.5
pepQ 2859394 p.Leu342Ser missense_variant 0.29
ribD 2986729 c.-110G>A upstream_gene_variant 0.4
Rv2752c 3065129 p.Leu355Met missense_variant 0.12
thyX 3068015 c.-70T>G upstream_gene_variant 0.12
thyA 3073806 c.666C>G synonymous_variant 0.25
fprA 3474631 p.Thr209Ala missense_variant 0.18
fbiB 3640767 c.-768C>T upstream_gene_variant 0.18
fbiA 3641140 p.Ile200Phe missense_variant 0.18
fbiB 3641758 p.Arg75Leu missense_variant 0.2
fbiB 3641866 p.Ser111Tyr missense_variant 0.22
fbiB 3642639 p.Glu369* stop_gained 0.17
clpC1 4039645 p.His354Asp missense_variant 0.33
clpC1 4039648 p.Glu353* stop_gained 0.29
clpC1 4039654 p.Thr351Ser missense_variant 0.29
clpC1 4040021 c.684A>T synonymous_variant 0.5
clpC1 4040144 c.561G>C synonymous_variant 0.33
embC 4240799 p.Tyr313His missense_variant 0.15
embC 4241021 p.Ala387Ser missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246548 p.Pro12Gln missense_variant 0.7
embB 4246555 c.42G>C synonymous_variant 0.83
embB 4246556 p.Ala15Pro missense_variant 0.83
embB 4246563 p.Leu17Trp missense_variant 0.8
embB 4246567 c.54G>T synonymous_variant 0.67
embB 4249375 c.2862G>T synonymous_variant 0.4
embB 4249480 c.2967G>T synonymous_variant 0.25
aftB 4267129 p.Ala570Ser missense_variant 0.22
aftB 4268150 p.Met229Ile missense_variant 0.33
ethR 4327177 c.-372C>A upstream_gene_variant 0.17
ethA 4327499 c.-26C>A upstream_gene_variant 0.18
ethR 4327757 p.Ala70Glu missense_variant 0.22
ethA 4327896 c.-423C>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0