TB-Profiler result

Run: SRR5535704
Summary

Run ID: SRR5535704

Sample name:

Date: 04-04-2023 10:38:32

Number of reads: 923091

Percentage reads mapped: 99.46

Strain: lineage4.3.3

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
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
pncA 2288751 p.Ser164* stop_gained 0.14 pyrazinamide
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 5188 c.-52C>A upstream_gene_variant 0.33
gyrB 5517 p.Ile93Thr missense_variant 0.2
gyrB 5724 p.Ala162Val missense_variant 0.14
gyrB 5772 p.Ala178Asp missense_variant 0.2
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8304 p.Thr335Pro missense_variant 0.22
gyrA 8994 p.Asp565Tyr missense_variant 0.67
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9569 p.Asp756Glu missense_variant 0.25
fgd1 490939 p.Phe53Leu missense_variant 1.0
fgd1 491150 p.Pro123Gln missense_variant 0.29
fgd1 491347 p.Gly189Ser missense_variant 0.2
fgd1 491561 p.His260Arg missense_variant 0.22
mshA 575627 p.Ala94Thr missense_variant 0.14
mshA 576125 p.Gly260* stop_gained 0.29
mshA 576391 c.1044G>T synonymous_variant 0.18
mshA 576636 p.Trp430Leu missense_variant 0.3
ccsA 620176 p.Val96Leu missense_variant 0.19
ccsA 620185 p.Gly99Cys missense_variant 0.14
ccsA 620755 p.Asp289Asn missense_variant 0.4
rpoB 760013 c.207C>T synonymous_variant 0.29
rpoB 760239 p.Thr145Ser missense_variant 0.25
rpoB 760250 p.Met148Ile missense_variant 0.18
rpoB 760272 p.Glu156* stop_gained 0.2
rpoB 760545 p.Gly247Trp missense_variant 1.0
rpoB 761282 c.1476C>A synonymous_variant 0.5
rpoB 762053 c.2247T>C synonymous_variant 0.2
rpoB 762174 p.Val790Phe missense_variant 0.2
rpoC 763771 p.Tyr134* stop_gained 0.22
rpoC 764253 p.Arg295Leu missense_variant 0.4
rpoC 764335 c.966G>T synonymous_variant 0.33
rpoC 764645 p.Gly426Cys missense_variant 0.18
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765301 c.1932C>T synonymous_variant 0.5
rpoC 766832 p.Glu1155* stop_gained 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775769 c.2712C>A synonymous_variant 0.25
mmpL5 776296 p.Gln729Glu missense_variant 0.33
mmpL5 777082 p.Lys467Gln missense_variant 0.4
mmpL5 777597 p.Arg295Leu missense_variant 0.67
mmpL5 777876 p.Arg202His missense_variant 0.17
mmpL5 778927 c.-447C>A upstream_gene_variant 0.22
mmpR5 779335 p.Asp116Tyr missense_variant 0.4
rplC 801029 p.Gly74Asp missense_variant 0.5
rplC 801080 p.Ala91Asp missense_variant 0.4
rplC 801394 p.Gly196Cys missense_variant 0.29
fbiC 1303149 c.219C>A synonymous_variant 0.17
fbiC 1304161 c.1235delG frameshift_variant 0.22
fbiC 1304467 p.Glu513Lys missense_variant 0.4
fbiC 1305294 p.Trp788Cys missense_variant 0.22
Rv1258c 1407245 p.Trp32Cys missense_variant 0.2
embR 1416771 p.Glu193* stop_gained 0.4
embR 1417510 c.-163C>A upstream_gene_variant 0.29
atpE 1460972 c.-73G>T upstream_gene_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473540 n.-118C>A upstream_gene_variant 0.5
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.5
fabG1 1673707 p.Gly90Ser missense_variant 0.67
inhA 1674427 p.Gly76Cys missense_variant 0.33
inhA 1674556 p.Gly119Cys missense_variant 0.25
inhA 1674684 p.Met161Ile missense_variant 0.25
rpsA 1834836 p.Met432Thr missense_variant 1.0
rpsA 1834958 p.Leu473Met missense_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918670 p.Arg244Leu missense_variant 0.25
ndh 2101887 p.Glu386* stop_gained 0.29
ndh 2101930 c.1113C>A synonymous_variant 0.5
ndh 2102162 p.Arg294Leu missense_variant 0.5
ndh 2102884 c.159G>T synonymous_variant 0.5
katG 2155019 p.Pro365Thr missense_variant 0.33
katG 2156196 c.-85C>T upstream_gene_variant 1.0
katG 2156271 c.-160G>T upstream_gene_variant 0.33
PPE35 2170103 c.510C>A synonymous_variant 0.22
PPE35 2170737 c.-125C>A upstream_gene_variant 0.33
PPE35 2170780 c.-168G>T upstream_gene_variant 0.4
Rv1979c 2221881 c.1284G>T synonymous_variant 0.5
Rv1979c 2222797 p.Pro123His missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288690 p.Cys184* stop_gained 0.18
pncA 2290033 c.-792C>A upstream_gene_variant 0.4
kasA 2518207 p.Ser31Arg missense_variant 0.33
kasA 2518896 p.Pro261Gln missense_variant 0.2
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714307 c.1026G>T synonymous_variant 0.5
eis 2714569 p.Ala255Asp missense_variant 0.5
eis 2714745 c.588C>A synonymous_variant 0.13
ahpC 2726776 p.Ala195Asp missense_variant 0.2
folC 2746340 p.Ala420Val missense_variant 1.0
folC 2746684 c.915C>A synonymous_variant 0.29
folC 2747072 p.Gly176Phe missense_variant 0.67
folC 2747284 c.315G>T synonymous_variant 0.22
folC 2747537 p.Pro21Gln missense_variant 0.4
pepQ 2860022 p.Glu133* stop_gained 0.18
ribD 2986835 c.-4G>T upstream_gene_variant 0.25
ribD 2987264 c.426G>T synonymous_variant 0.22
Rv2752c 3066027 c.165C>A synonymous_variant 0.22
Rv2752c 3066356 c.-165G>T upstream_gene_variant 0.13
thyX 3067377 p.Arg190Pro missense_variant 0.22
thyA 3073868 p.Thr202Ala missense_variant 1.0
fbiD 3339124 p.Gly3Cys missense_variant 0.33
fbiD 3339214 p.Gln33* stop_gained 0.18
fbiD 3339235 p.Leu40Met missense_variant 0.2
Rv3083 3449299 p.Arg266Trp missense_variant 0.29
Rv3083 3449537 p.Ala345Glu missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474096 p.Glu30Asp missense_variant 0.29
fprA 3475222 p.Val406Leu missense_variant 0.22
fprA 3475313 p.Pro436Gln missense_variant 0.14
Rv3236c 3612403 c.714G>T synonymous_variant 0.29
Rv3236c 3613084 c.33C>A synonymous_variant 0.5
fbiB 3640716 c.-819C>A upstream_gene_variant 0.33
fbiB 3641397 c.-138G>T upstream_gene_variant 0.5
alr 3840896 p.Met175Ile missense_variant 0.25
ddn 3986649 c.-195G>T upstream_gene_variant 0.29
ddn 3986802 c.-42G>A upstream_gene_variant 0.5
ddn 3986882 c.39C>A synonymous_variant 0.67
ddn 3986990 c.147G>A synonymous_variant 0.33
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038875 c.1830C>A synonymous_variant 0.17
panD 4044425 c.-144C>A upstream_gene_variant 0.22
embC 4240033 c.171G>T synonymous_variant 0.29
embC 4240133 p.Ala91Thr missense_variant 0.29
embC 4240577 p.Ala239Ser missense_variant 0.14
embC 4240807 c.945C>A synonymous_variant 0.18
embC 4240836 p.Gly325Val missense_variant 0.22
embC 4240850 p.Leu330Met missense_variant 0.18
embC 4241074 c.1212G>T synonymous_variant 0.18
embC 4241581 c.1719C>A synonymous_variant 0.4
embC 4241611 c.1749G>T synonymous_variant 0.67
embC 4242426 p.Arg855Gln missense_variant 0.22
embC 4242619 p.Asp919Glu missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244086 p.Pro285Gln missense_variant 0.2
embA 4244279 c.1047G>A synonymous_variant 0.18
embB 4246796 p.Gly95Cys missense_variant 0.22
embB 4247009 p.Asp166Tyr missense_variant 0.18
embB 4247059 c.546C>T synonymous_variant 0.14
embB 4247560 p.Trp349Cys missense_variant 0.2
embB 4248317 p.Val602Leu missense_variant 0.22
embB 4248466 p.Ser651Arg missense_variant 0.22
aftB 4268655 p.Thr61Ile missense_variant 0.22
ubiA 4269855 c.-22G>T upstream_gene_variant 0.22
ubiA 4269935 c.-102C>A upstream_gene_variant 0.18
ethR 4326940 c.-609G>T upstream_gene_variant 0.33
ethA 4328412 c.-939G>T upstream_gene_variant 0.15
ethA 4328470 c.-997G>C upstream_gene_variant 0.15
whiB6 4338277 p.Pro82His missense_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0