TB-Profiler result

Run: SRR21673295
Summary

Run ID: SRR21673295

Sample name:

Date: 04-04-2023 02:33:32

Number of reads: 298745

Percentage reads mapped: 99.34

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 2155058 c.1053delG frameshift_variant 0.18 isoniazid
katG 2155385 p.Ala243Ser missense_variant 0.11 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 5355 p.Glu39Gly missense_variant 0.22
gyrB 5791 c.552A>G synonymous_variant 0.12
gyrB 5960 p.Thr241Ala missense_variant 0.13
gyrB 6088 c.849C>T synonymous_variant 0.15
gyrB 6881 p.Leu548Val missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7884 p.Arg195Ser missense_variant 0.18
gyrA 8014 p.Gln238Arg missense_variant 0.29
gyrA 8290 p.Asn330Thr missense_variant 0.14
gyrA 8377 p.Asp359Gly missense_variant 0.2
mshA 576584 p.Arg413Trp missense_variant 0.4
mshA 576751 p.Lys468Asn missense_variant 0.2
ccsA 620297 p.Pro136Gln missense_variant 0.2
rpoB 760646 c.840C>A synonymous_variant 0.17
rpoB 760875 p.Val357Met missense_variant 0.22
rpoB 761157 p.Ala451Ser missense_variant 0.15
rpoB 761275 p.Leu490Pro missense_variant 0.29
rpoB 761403 p.His533Tyr missense_variant 0.25
rpoB 762092 p.Glu762Asp missense_variant 0.14
rpoB 762135 p.Asp777Tyr missense_variant 0.18
rpoB 762574 p.Gly923Asp missense_variant 0.18
rpoB 762847 p.Pro1014Arg missense_variant 0.22
rpoC 763265 c.-105G>A upstream_gene_variant 0.12
rpoC 764901 p.Ala511Asp missense_variant 0.14
rpoC 764994 p.Ala542Asp missense_variant 0.18
rpoC 765859 p.Glu830Asp missense_variant 0.18
rpoC 766478 p.Ala1037Ser missense_variant 0.12
rpoC 767198 p.Glu1277* stop_gained 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776552 p.Gln643His missense_variant 0.17
mmpL5 776666 p.Asp605Glu missense_variant 0.2
mmpL5 776829 p.His551Arg missense_variant 0.18
mmpL5 778036 p.Val149Phe missense_variant 0.17
mmpR5 779420 p.Ala144Glu missense_variant 0.2
mmpS5 779581 c.-676G>T upstream_gene_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781610 c.53delA frameshift_variant 0.12
fbiC 1302779 c.-152C>G upstream_gene_variant 0.29
fbiC 1303090 p.Glu54* stop_gained 0.18
fbiC 1303135 p.Gly69Arg missense_variant 0.15
fbiC 1303260 c.330G>T synonymous_variant 0.11
fbiC 1303670 p.Asp247Gly missense_variant 0.15
fbiC 1303737 c.807G>A synonymous_variant 0.11
fbiC 1304128 p.Gln400Lys missense_variant 0.15
fbiC 1304672 p.Val581Asp missense_variant 0.25
fbiC 1304769 c.1839C>T synonymous_variant 0.2
fbiC 1304788 p.Ala620Ser missense_variant 0.2
fbiC 1304841 p.Glu637Asp missense_variant 0.14
Rv1258c 1406406 p.Pro312Gln missense_variant 0.22
Rv1258c 1407123 p.Arg73Leu missense_variant 0.4
embR 1416294 p.Val352Leu missense_variant 0.12
embR 1417179 p.Thr57Ser missense_variant 0.14
embR 1417294 c.54A>G synonymous_variant 0.25
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
atpE 1461104 c.60C>A synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472717 n.874_875dupGC non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474030 n.373G>A non_coding_transcript_exon_variant 0.15
rrl 1474850 n.1193C>A non_coding_transcript_exon_variant 0.12
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.15
rrl 1476611 n.2954T>A non_coding_transcript_exon_variant 0.12
fabG1 1673392 c.-48G>C upstream_gene_variant 0.1
fabG1 1673420 c.-20C>A upstream_gene_variant 0.12
inhA 1674737 p.Ala179Asp missense_variant 0.18
inhA 1674965 p.Gly255Val missense_variant 0.22
rpsA 1834216 c.675C>T synonymous_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918206 c.267G>T synonymous_variant 0.22
tlyA 1918575 c.636G>T synonymous_variant 0.29
tlyA 1918741 p.Pro268Ala missense_variant 0.18
ndh 2101776 p.Ser423Gly missense_variant 0.13
ndh 2101969 c.1074G>A synonymous_variant 0.12
ndh 2102557 p.Ser162Arg missense_variant 0.12
ndh 2102664 p.Gly127Ser missense_variant 0.14
ndh 2102855 p.Ile63Asn missense_variant 0.12
katG 2154006 c.2106G>A synonymous_variant 0.25
katG 2155073 p.Pro347Thr missense_variant 0.2
katG 2155506 c.606C>A synonymous_variant 0.11
katG 2155711 p.Ser134Ile missense_variant 0.18
katG 2155852 p.Ser87* stop_gained 0.14
katG 2156490 c.-379G>T upstream_gene_variant 0.12
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168222 c.2391G>T synonymous_variant 0.14
PPE35 2168416 p.Gly733Trp missense_variant 0.13
PPE35 2168456 c.2157C>G synonymous_variant 0.13
PPE35 2169161 c.1452G>T synonymous_variant 0.12
PPE35 2169721 p.Gly298Ser missense_variant 0.12
PPE35 2169734 c.879C>A synonymous_variant 0.13
PPE35 2170527 p.Ser29Val missense_variant 0.22
PPE35 2170717 c.-105C>G upstream_gene_variant 0.22
PPE35 2170753 c.-141T>C upstream_gene_variant 0.25
PPE35 2170811 c.-199C>A upstream_gene_variant 0.25
Rv1979c 2221821 c.1344G>T synonymous_variant 0.12
Rv1979c 2222325 c.840C>T synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288859 p.Val128Ala missense_variant 0.12
pncA 2289100 p.Lys48Gln missense_variant 0.15
pncA 2289287 c.-46C>A upstream_gene_variant 0.5
pncA 2289554 c.-313G>T upstream_gene_variant 0.12
kasA 2518141 c.27C>T synonymous_variant 0.18
ahpC 2726561 c.369T>C synonymous_variant 0.25
folC 2746548 p.Asp351His missense_variant 0.29
pepQ 2859364 p.Pro352Leu missense_variant 0.13
pepQ 2860368 c.51C>A synonymous_variant 0.22
ribD 2986681 c.-158A>G upstream_gene_variant 0.14
Rv2752c 3064789 p.Leu468* stop_gained 0.22
Rv2752c 3065009 p.Pro395Ser missense_variant 0.18
Rv2752c 3065026 p.Arg389Gln missense_variant 0.15
Rv2752c 3065043 p.Phe383Leu missense_variant 0.15
Rv2752c 3065233 p.Arg320His missense_variant 0.15
thyX 3067491 p.Ala152Asp missense_variant 0.22
thyX 3067965 c.-20C>T upstream_gene_variant 0.2
thyX 3067984 c.-39C>T upstream_gene_variant 0.25
thyA 3074253 p.His73Gln missense_variant 0.12
thyA 3074280 c.192C>A synonymous_variant 0.11
thyA 3074357 p.Ser39Thr missense_variant 0.12
ald 3086625 c.-195G>T upstream_gene_variant 0.11
ald 3087016 p.Ala66Val missense_variant 0.25
Rv3083 3448395 c.-109T>A upstream_gene_variant 0.22
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
fprA 3473840 c.-167G>A upstream_gene_variant 0.11
fprA 3473912 c.-95T>G upstream_gene_variant 0.13
fprA 3474530 p.Arg175Leu missense_variant 0.15
whiB7 3568623 c.57G>A synonymous_variant 0.12
Rv3236c 3612740 p.Tyr126Phe missense_variant 0.17
Rv3236c 3613070 p.Ala16Glu missense_variant 0.15
fbiB 3641085 c.-450G>A upstream_gene_variant 0.17
fbiB 3641564 c.30G>T synonymous_variant 0.22
fbiB 3641651 p.Trp39Cys missense_variant 0.33
fbiB 3642660 p.Ala376Ser missense_variant 0.25
alr 3840889 p.Ala178Pro missense_variant 0.17
alr 3841017 p.Leu135Arg missense_variant 0.67
alr 3841406 p.Trp5Cys missense_variant 0.13
rpoA 3877847 p.Leu221Met missense_variant 0.33
ddn 3986711 c.-133C>A upstream_gene_variant 0.15
ddn 3986731 c.-113A>G upstream_gene_variant 0.12
clpC1 4038430 p.Leu759Met missense_variant 0.15
clpC1 4038974 c.1731T>C synonymous_variant 0.18
clpC1 4039105 p.Arg534Ser missense_variant 0.2
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040093 c.612C>T synonymous_variant 1.0
panD 4044109 c.172delT frameshift_variant 0.13
embC 4241511 p.Met550Thr missense_variant 0.17
embC 4241856 p.Leu665His missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243035 p.Gly1058Val missense_variant 0.33
embC 4243140 p.Arg1093Leu missense_variant 0.14
embA 4243413 p.Pro61Thr missense_variant 0.14
embA 4243851 p.Met207Val missense_variant 0.22
embA 4244099 c.867T>C synonymous_variant 0.14
embB 4246916 p.Val135Met missense_variant 0.33
embB 4248048 p.Ile512Asn missense_variant 0.18
aftB 4267290 p.Ala516Glu missense_variant 0.22
aftB 4267528 p.Ala437Ser missense_variant 0.18
aftB 4267586 c.1251C>A synonymous_variant 0.15
aftB 4267798 p.Leu347Met missense_variant 0.15
aftB 4267950 p.Pro296His missense_variant 0.4
ubiA 4268984 c.849delA frameshift_variant 0.14
aftB 4269681 c.-845G>T upstream_gene_variant 0.33
ethA 4326719 p.Ala252Asp missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407629 p.Gly192Cys missense_variant 0.33
gid 4407774 c.429C>T synonymous_variant 0.22
gid 4408079 p.Gly42Arg missense_variant 0.14
gid 4408185 c.18C>A synonymous_variant 0.2
gid 4408258 c.-56C>G upstream_gene_variant 0.13
gid 4408273 c.-71C>T upstream_gene_variant 0.14
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0