TB-Profiler result

Run: SRR4035769
Summary

Run ID: SRR4035769

Sample name:

Date: 04-04-2023 07:17:15

Number of reads: 1101080

Percentage reads mapped: 99.42

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;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
katG 2154407 c.1703delC frameshift_variant 0.18 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
gyrB 5113 c.-127G>T upstream_gene_variant 0.13
gyrA 7331 c.30C>T synonymous_variant 0.12
gyrA 7362 p.Glu21Arg missense_variant 1.0
gyrA 7419 p.Ala40Ser missense_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8019 p.Thr240Ala missense_variant 0.12
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9067 p.Arg589Gln missense_variant 0.13
gyrA 9139 p.Gln613Arg missense_variant 0.14
gyrA 9295 p.Cys665Tyr missense_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490904 p.Phe41Ser missense_variant 0.25
fgd1 491013 c.231C>A synonymous_variant 0.14
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 576623 p.Ala426Thr missense_variant 0.15
mshA 576690 p.Tyr448Cys missense_variant 0.13
ccsA 620632 p.Ala248Ser missense_variant 0.18
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760179 p.Ala125Thr missense_variant 0.13
rpoB 760405 p.Pro200Arg missense_variant 0.13
rpoB 761467 p.Leu554Gln missense_variant 0.18
rpoB 761827 p.His674Arg missense_variant 0.12
rpoB 761876 c.2070C>T synonymous_variant 0.12
rpoB 761880 c.2076delC frameshift_variant 0.13
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764828 p.Leu487Val missense_variant 0.12
rpoC 764862 p.Leu498Pro missense_variant 0.12
rpoC 765094 c.1725C>G synonymous_variant 0.11
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765787 c.2418C>A synonymous_variant 0.14
rpoC 766367 p.Ala1000Pro missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776192 c.2289G>A synonymous_variant 0.12
mmpL5 776345 p.Asp712Glu missense_variant 0.12
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777725 p.Phe252Leu missense_variant 0.13
mmpL5 778917 c.-437A>G upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302843 c.-88A>T upstream_gene_variant 0.13
fbiC 1303016 p.Val29Gly missense_variant 0.13
fbiC 1303030 p.Arg34* stop_gained 0.14
Rv1258c 1406117 c.1224A>G synonymous_variant 0.12
Rv1258c 1406210 p.His377Gln missense_variant 0.14
Rv1258c 1406349 p.Ile331Ser missense_variant 0.2
embR 1416329 p.Val340Ala missense_variant 0.1
embR 1416336 p.Asn338Asp missense_variant 0.12
embR 1416436 c.912A>G synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673273 c.-167C>T upstream_gene_variant 0.14
fabG1 1673905 p.Ser156Pro missense_variant 0.14
inhA 1674184 c.-18C>T upstream_gene_variant 0.12
inhA 1674203 c.2T>A start_lost 0.14
tlyA 1917920 c.-20G>C upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102861 p.Gly61Ala missense_variant 0.12
katG 2154220 p.Leu631Pro missense_variant 0.2
katG 2155943 p.Pro57Ser missense_variant 0.29
katG 2155997 p.Trp39Arg missense_variant 0.17
PPE35 2167773 p.Gly947Asp missense_variant 0.17
PPE35 2167840 p.Val925Phe missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289957 c.-716G>A upstream_gene_variant 0.29
pncA 2289973 c.-733delG upstream_gene_variant 0.33
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
eis 2714220 c.1113C>T synonymous_variant 0.22
eis 2714223 c.1110C>A synonymous_variant 0.22
eis 2714230 p.Thr368Met missense_variant 0.25
eis 2715302 p.Asp11His missense_variant 0.12
eis 2715316 p.Cys6Ser missense_variant 0.11
eis 2715552 c.-220A>G upstream_gene_variant 0.12
ahpC 2726529 p.Asp113Asn missense_variant 0.15
folC 2746178 p.Thr474Ile missense_variant 0.12
folC 2746235 c.1363delG frameshift_variant 0.15
folC 2746528 c.1071C>G synonymous_variant 0.11
folC 2746609 p.Phe330Leu missense_variant 0.11
folC 2747643 c.-45G>A upstream_gene_variant 0.14
folC 2747708 c.-110G>A upstream_gene_variant 0.15
pepQ 2859789 c.630G>C synonymous_variant 0.2
pepQ 2859826 c.592delG frameshift_variant 0.29
pepQ 2860170 c.249G>A synonymous_variant 0.22
pepQ 2860456 c.-38G>T upstream_gene_variant 0.15
ribD 2986801 c.-38G>A upstream_gene_variant 0.13
ribD 2987282 c.444C>T synonymous_variant 0.14
Rv2752c 3064543 p.Met550Lys missense_variant 0.14
Rv2752c 3065793 c.399C>T synonymous_variant 0.15
Rv2752c 3065917 p.Phe92Ser missense_variant 0.12
Rv2752c 3067064 c.-873A>G upstream_gene_variant 0.1
thyX 3067360 c.584_585dupTC frameshift_variant 0.15
thyX 3067443 p.Arg168His missense_variant 0.14
thyX 3067830 p.Ala39Gly missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448417 c.-87C>G upstream_gene_variant 0.15
Rv3083 3449342 p.Ser280Phe missense_variant 0.15
fprA 3473906 c.-101A>G upstream_gene_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474363 c.357G>C synonymous_variant 0.12
fprA 3474754 p.Lys250Glu missense_variant 0.12
fprA 3475017 p.Gln337His missense_variant 0.2
fprA 3475072 p.Val356Leu missense_variant 0.29
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612785 p.Leu111* stop_gained 0.14
fbiA 3641283 p.Ile247Met missense_variant 0.14
fbiA 3641290 p.Lys250Glu missense_variant 0.14
fbiB 3641508 c.-27C>A upstream_gene_variant 0.17
fbiB 3642272 c.738C>G synonymous_variant 0.12
alr 3840593 c.828C>T synonymous_variant 0.13
ddn 3986844 c.1A>T initiator_codon_variant 0.12
clpC1 4040211 p.Pro165Arg missense_variant 0.11
panD 4043924 p.Asp120Asn missense_variant 0.14
panD 4043939 p.Ile115Phe missense_variant 0.18
embC 4241568 p.Ile569Thr missense_variant 0.12
embC 4241736 p.Val625Gly missense_variant 0.17
embC 4242320 p.Pro820Thr missense_variant 0.18
embC 4242366 p.Ser835Phe missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243269 p.Ala13Thr missense_variant 0.15
embA 4244449 p.Ala406Val missense_variant 0.14
embA 4244740 p.Tyr503Cys missense_variant 0.14
embA 4245239 c.2007C>T synonymous_variant 0.12
embA 4245488 c.2256G>C synonymous_variant 0.14
embB 4247580 p.Ala356Asp missense_variant 0.12
embB 4248468 p.Tyr652Cys missense_variant 0.12
embB 4248779 c.2267delA frameshift_variant 0.12
aftB 4267297 p.Leu514Met missense_variant 0.17
aftB 4267932 p.Ala302Val missense_variant 0.18
aftB 4268362 p.Ser159Pro missense_variant 0.14
ubiA 4269013 p.Pro274Arg missense_variant 0.11
ubiA 4269673 p.Lys54Met missense_variant 0.2
ubiA 4269913 c.-80T>G upstream_gene_variant 0.11
ethA 4326730 c.741_743delGGC disruptive_inframe_deletion 0.12
whiB6 4338347 p.Arg59Trp missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338604 c.-83G>A upstream_gene_variant 0.12
gid 4407656 p.Ala183Thr missense_variant 0.14