TB-Profiler result

Run: SRR21677896
Summary

Run ID: SRR21677896

Sample name:

Date: 04-04-2023 02:49:46

Number of reads: 298454

Percentage reads mapped: 98.4

Strain: lineage4.8

Drug-resistance: Other

Download CSV Download TXT Download PDF Download JSON
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
pncA 2288883 p.Leu120Gln missense_variant 0.18 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 5476 p.Asp79Glu missense_variant 0.18
gyrB 5795 p.Asp186Asn missense_variant 0.22
gyrB 6233 p.Ala332Ser missense_variant 0.25
gyrB 6483 p.Gln415Arg missense_variant 0.25
gyrB 6979 p.Phe580Leu missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7758 p.Ile153Phe missense_variant 0.18
gyrA 9071 c.1770G>A synonymous_variant 0.17
gyrA 9696 c.2396_2397delAG frameshift_variant 1.0
mshA 575550 p.Met68Thr missense_variant 0.2
ccsA 619706 c.-185G>T upstream_gene_variant 0.17
ccsA 619713 c.-178C>T upstream_gene_variant 0.2
rpoB 759883 p.Val26Glu missense_variant 0.29
rpoB 760208 c.404delA frameshift_variant 0.14
rpoB 760664 c.858G>T synonymous_variant 0.29
rpoB 760861 p.Pro352Gln missense_variant 0.2
rpoB 760987 p.Val394Ala missense_variant 0.33
rpoB 761128 p.Ser441* stop_gained 1.0
rpoB 762159 p.Arg785Ser missense_variant 0.18
rpoB 762234 p.Pro810Ser missense_variant 0.14
rpoB 762586 p.Glu927Gly missense_variant 0.33
rpoB 762988 p.Arg1061Gln missense_variant 0.17
rpoB 763302 p.Ala1166Ser missense_variant 0.2
rpoC 764127 p.Thr253Asn missense_variant 0.33
rpoC 765316 p.Glu649Asp missense_variant 0.15
rpoC 765401 p.Pro678Thr missense_variant 0.2
rpoC 765614 p.Tyr749His missense_variant 0.11
rpoC 765645 p.Gln759Pro missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776281 p.Arg734Ser missense_variant 0.12
mmpL5 776976 p.Ser502Ile missense_variant 0.15
mmpL5 777092 p.Leu463Phe missense_variant 0.15
mmpL5 777215 c.1266C>G synonymous_variant 0.11
mmpL5 777437 c.1044C>T synonymous_variant 0.22
mmpL5 777893 p.Gln196His missense_variant 0.4
mmpL5 778922 c.-442G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781437 c.-123G>A upstream_gene_variant 0.11
fbiC 1302814 c.-117C>A upstream_gene_variant 0.4
fbiC 1302852 c.-78delT upstream_gene_variant 0.4
fbiC 1304083 p.Gly385Cys missense_variant 0.2
fbiC 1305164 p.Val745Ala missense_variant 0.17
Rv1258c 1406290 p.Val351Met missense_variant 0.18
embR 1416876 p.Phe158Leu missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472105 n.260T>G non_coding_transcript_exon_variant 0.13
rrs 1472317 n.472G>T non_coding_transcript_exon_variant 0.25
rrs 1472433 n.588G>A non_coding_transcript_exon_variant 0.15
rrs 1472842 n.997G>T non_coding_transcript_exon_variant 0.12
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475113 n.1456C>A non_coding_transcript_exon_variant 0.2
rrl 1475442 n.1785C>T non_coding_transcript_exon_variant 0.14
rrl 1475879 n.2222T>C non_coding_transcript_exon_variant 0.11
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
fabG1 1673321 c.-119A>G upstream_gene_variant 0.14
fabG1 1674161 p.Gly241Val missense_variant 0.2
inhA 1674384 c.183C>T synonymous_variant 0.4
inhA 1674840 c.639C>G synonymous_variant 0.33
rpsA 1833738 p.Arg66His missense_variant 0.11
rpsA 1833940 c.399C>T synonymous_variant 0.14
rpsA 1833968 p.Gly143Trp missense_variant 0.11
rpsA 1834220 p.Asp227Tyr missense_variant 0.14
rpsA 1834568 p.Asp343Tyr missense_variant 0.5
rpsA 1834884 p.Gln448Arg missense_variant 0.5
tlyA 1917815 c.-125C>G upstream_gene_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918723 p.Arg262Cys missense_variant 0.2
ndh 2102069 p.Ala325Asp missense_variant 0.33
ndh 2103013 c.30A>G synonymous_variant 0.17
katG 2154818 p.Pro432Thr missense_variant 0.2
katG 2155384 p.Ala243Asp missense_variant 0.25
katG 2155787 p.Ala109Pro missense_variant 0.25
PPE35 2167691 c.2922C>A synonymous_variant 0.17
PPE35 2168027 c.2586C>A synonymous_variant 0.4
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2168318 c.2295T>A synonymous_variant 0.14
PPE35 2168831 c.1782C>A synonymous_variant 0.25
PPE35 2169173 p.Ile480Met missense_variant 0.15
PPE35 2169220 c.1393C>T synonymous_variant 0.14
PPE35 2169407 p.Phe402Leu missense_variant 0.15
PPE35 2169433 p.Pro394Ser missense_variant 0.18
PPE35 2169569 p.Ser348Arg missense_variant 0.13
PPE35 2169820 p.Asn265Asp missense_variant 0.13
PPE35 2169853 p.Gly254Cys missense_variant 0.12
PPE35 2170394 c.219G>T synonymous_variant 0.5
PPE35 2170518 p.Asp32Thr missense_variant 0.5
PPE35 2170540 c.73C>T synonymous_variant 0.5
Rv1979c 2222010 p.Gln385His missense_variant 0.17
Rv1979c 2222073 c.1092G>T synonymous_variant 0.22
Rv1979c 2222319 c.846C>A synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288903 c.339C>A synonymous_variant 0.12
pncA 2290114 c.-873T>C upstream_gene_variant 0.2
eis 2714666 p.Tyr223His missense_variant 0.11
eis 2715304 p.Glu10Gly missense_variant 0.12
ahpC 2726327 c.135C>A synonymous_variant 0.17
ahpC 2726734 p.Gly181Asp missense_variant 0.14
folC 2746268 p.Thr444Asn missense_variant 0.17
folC 2746334 p.Gly422Val missense_variant 0.17
folC 2746601 p.Val333Gly missense_variant 0.5
pepQ 2859322 p.Pro366His missense_variant 0.2
pepQ 2859346 p.Thr358Asn missense_variant 0.14
pepQ 2859415 p.Gly335Asp missense_variant 0.12
pepQ 2859832 c.586delG frameshift_variant 0.2
pepQ 2860027 p.Leu131Pro missense_variant 0.17
ribD 2987132 p.Met98Ile missense_variant 0.22
Rv2752c 3064797 c.1395G>A synonymous_variant 0.5
Rv2752c 3064909 p.Ser428Ile missense_variant 0.2
Rv2752c 3065245 p.Ser316* stop_gained 0.14
Rv2752c 3065361 c.831C>A synonymous_variant 0.12
thyX 3067331 p.Asp205Glu missense_variant 0.5
thyX 3067560 p.Arg129His missense_variant 0.17
ald 3087146 p.Asp109Glu missense_variant 0.12
ald 3087156 p.Thr113Ser missense_variant 0.12
ald 3087276 c.459delA frameshift_variant 0.18
ald 3087445 p.Ala209Asp missense_variant 0.12
fprA 3474044 p.Pro13Gln missense_variant 0.67
Rv3236c 3613029 c.88T>C synonymous_variant 0.2
Rv3236c 3613301 c.-185G>T upstream_gene_variant 0.12
fbiA 3640718 p.Cys59Tyr missense_variant 0.14
fbiB 3641160 c.-375C>T upstream_gene_variant 0.17
fbiB 3641235 c.-300G>A upstream_gene_variant 0.15
alr 3840972 p.Arg150Leu missense_variant 0.2
alr 3840989 c.432G>T synonymous_variant 0.25
alr 3841437 c.-17G>A upstream_gene_variant 0.11
rpoA 3877536 c.972C>T synonymous_variant 0.17
rpoA 3877925 p.Asp195Tyr missense_variant 0.17
clpC1 4038808 p.Glu633* stop_gained 0.22
clpC1 4038856 p.Lys617Glu missense_variant 0.4
clpC1 4039574 c.1131G>A synonymous_variant 0.2
clpC1 4039699 p.Ala336Ser missense_variant 0.15
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4039866 p.Gly280Asp missense_variant 0.14
clpC1 4040475 p.His77Arg missense_variant 0.25
embC 4240044 p.Trp61Leu missense_variant 0.29
embC 4241131 c.1271dupC frameshift_variant 0.17
embC 4241158 c.1296T>C synonymous_variant 0.12
embC 4241978 p.Ser706Pro missense_variant 0.29
embC 4242082 p.Asn740Lys missense_variant 0.2
embC 4242473 p.Leu871Met missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243077 p.Pro1072His missense_variant 0.17
embA 4243679 c.447C>A synonymous_variant 0.18
embA 4243973 c.741A>T synonymous_variant 0.18
embA 4243992 p.Asp254Asn missense_variant 0.14
embA 4244268 c.1038dupG frameshift_variant 0.15
embA 4245757 p.Ser842Ile missense_variant 0.12
embA 4246024 p.Trp931Leu missense_variant 0.15
embA 4246060 p.Ala943Asp missense_variant 0.17
embB 4246754 p.Ala81Ser missense_variant 0.13
embB 4248139 c.1626C>A synonymous_variant 0.17
embB 4248292 c.1779G>T synonymous_variant 0.12
aftB 4266986 c.1851T>C synonymous_variant 0.17
aftB 4267168 p.Gln557* stop_gained 0.14
aftB 4268776 c.60dupG frameshift_variant 0.25
aftB 4268870 c.-34G>T upstream_gene_variant 0.2
ubiA 4269293 p.Ala181Ser missense_variant 0.25
ethA 4326722 p.Ser251Ile missense_variant 0.12
ethR 4327673 p.Leu42Gln missense_variant 0.14
whiB6 4338463 p.Asp20Val missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407709 p.Glu165Gly missense_variant 0.15
gid 4407983 c.219dupG frameshift_variant 0.14
gid 4408138 p.Tyr22Cys missense_variant 0.4