TB-Profiler result

Run: SRR6896296
Summary

Run ID: SRR6896296

Sample name:

Date: 04-04-2023 18:01:31

Number of reads: 229132

Percentage reads mapped: 97.5

Strain: lineage2

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
lineage2 East-Asian Beijing RD105 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 761076 p.Phe424Leu missense_variant 0.4 rifampicin
ethA 4327166 c.306_307delCA frameshift_variant 0.13 ethionamide
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 5370 p.His44Pro missense_variant 0.15
gyrB 5689 c.450T>C synonymous_variant 0.18
gyrB 5830 p.Met197Ile missense_variant 0.14
gyrB 6158 p.Thr307Ala missense_variant 0.25
gyrA 6346 c.-956C>T upstream_gene_variant 0.15
gyrB 6524 p.Arg429Ser missense_variant 0.11
gyrB 7025 p.Lys596Glu missense_variant 0.17
gyrA 7317 c.16T>C synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8353 p.Gly351Val missense_variant 0.33
gyrA 8649 p.Arg450Cys missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9762 p.Glu821* stop_gained 0.5
fgd1 491006 p.Leu75Arg missense_variant 0.22
fgd1 491043 c.261T>C synonymous_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620267 p.Ala126Glu missense_variant 0.22
ccsA 620388 c.498A>G synonymous_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620647 c.759delA frameshift_variant 0.5
ccsA 620703 c.813G>A synonymous_variant 0.4
rpoB 759788 c.-19A>G upstream_gene_variant 0.14
rpoB 759999 p.Arg65Gly missense_variant 0.14
rpoB 760405 p.Pro200Gln missense_variant 0.22
rpoB 760868 c.1062C>A synonymous_variant 0.5
rpoB 761229 p.Gly475Cys missense_variant 0.2
rpoB 761723 c.1917A>G synonymous_variant 0.2
rpoB 762835 p.Gly1010Asp missense_variant 0.25
rpoC 762971 c.-399G>A upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763646 p.Gly93Ser missense_variant 0.2
rpoC 763809 p.Glu147Ala missense_variant 0.25
rpoC 765846 p.Asn826Ser missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776797 p.Val562Ile missense_variant 0.11
mmpR5 778070 c.-920G>A upstream_gene_variant 0.33
mmpL5 778959 c.-479T>C upstream_gene_variant 0.13
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
mmpS5 779656 c.-751G>T upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781428 c.-132C>A upstream_gene_variant 0.29
rplC 800660 c.-148delA upstream_gene_variant 0.22
fbiC 1303309 p.Glu127* stop_gained 0.13
fbiC 1303404 c.474A>G synonymous_variant 0.18
fbiC 1304263 p.Gly445Cys missense_variant 0.29
fbiC 1304669 p.Ser580Leu missense_variant 0.18
fbiC 1305207 c.2277C>A synonymous_variant 0.38
fbiC 1305243 c.2313T>C synonymous_variant 0.33
fbiC 1305268 p.Arg780Ser missense_variant 0.33
fbiC 1305272 p.Ile781Thr missense_variant 0.33
fbiC 1305481 p.Tyr851Asn missense_variant 0.25
Rv1258c 1406107 p.Asp412Asn missense_variant 0.22
Rv1258c 1406291 c.1050G>T synonymous_variant 0.33
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406827 p.Thr172Ala missense_variant 0.25
Rv1258c 1407313 p.Phe10Val missense_variant 0.13
embR 1416291 c.1055_1056dupTG frameshift_variant 0.15
embR 1416383 c.964delA frameshift_variant 0.25
embR 1416632 c.715delC frameshift_variant 0.25
embR 1417460 c.-113G>C upstream_gene_variant 0.67
atpE 1461193 p.Phe50Ser missense_variant 0.17
atpE 1461220 p.Leu59Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471790 n.-56T>C upstream_gene_variant 0.12
rrs 1472072 n.227A>G non_coding_transcript_exon_variant 0.18
rrs 1472499 n.654A>G non_coding_transcript_exon_variant 0.2
rrs 1472530 n.685G>T non_coding_transcript_exon_variant 0.2
rrs 1472677 n.834delT non_coding_transcript_exon_variant 0.22
rrl 1474005 n.348T>G non_coding_transcript_exon_variant 0.17
rrl 1474115 n.458C>A non_coding_transcript_exon_variant 0.33
rrl 1474195 n.538A>G non_coding_transcript_exon_variant 0.33
rrl 1474265 n.608G>A non_coding_transcript_exon_variant 0.4
rrl 1474305 n.649delA non_coding_transcript_exon_variant 0.18
rrl 1474810 n.1153G>T non_coding_transcript_exon_variant 0.25
rrl 1474921 n.1268delG non_coding_transcript_exon_variant 0.22
rrl 1475001 n.1344A>G non_coding_transcript_exon_variant 0.33
rrl 1475387 n.1733delA non_coding_transcript_exon_variant 0.12
rrl 1475593 n.1941delG non_coding_transcript_exon_variant 0.5
rrl 1475627 n.1970G>T non_coding_transcript_exon_variant 0.18
rrl 1475635 n.1978G>T non_coding_transcript_exon_variant 0.18
rrl 1476065 n.2408A>G non_coding_transcript_exon_variant 0.11
fabG1 1673315 c.-125_-124insGG upstream_gene_variant 0.67
fabG1 1674183 c.744A>G stop_lost&splice_region_variant 0.29
rpsA 1833646 c.105T>C synonymous_variant 1.0
rpsA 1834170 c.631_633delATC conservative_inframe_deletion 0.2
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1918739 p.Gly267Val missense_variant 0.25
ndh 2102620 c.423C>A synonymous_variant 0.25
ndh 2102821 c.222C>A synonymous_variant 0.18
ndh 2102838 p.Ala69Ser missense_variant 0.22
katG 2154163 p.Ser650Tyr missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168697 p.Ile639Thr missense_variant 0.13
PPE35 2168801 c.1812A>G synonymous_variant 0.13
PPE35 2169092 c.1521G>T synonymous_variant 0.29
PPE35 2169675 p.Asn313Ser missense_variant 0.11
Rv1979c 2221724 p.Arg481Gly missense_variant 0.22
Rv1979c 2221822 p.Ser448* stop_gained 0.15
Rv1979c 2221863 p.Tyr434* stop_gained 0.17
Rv1979c 2222129 p.Tyr346His missense_variant 0.2
Rv1979c 2222570 p.Ala199Ser missense_variant 0.14
Rv1979c 2223002 p.Gly55Arg missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288865 p.Asp126Val missense_variant 0.25
pncA 2289831 c.-590A>G upstream_gene_variant 0.5
kasA 2517943 c.-172A>G upstream_gene_variant 0.18
kasA 2518259 p.Glu49* stop_gained 0.33
eis 2714195 p.Ser380Pro missense_variant 0.18
eis 2714659 p.Leu225Pro missense_variant 0.4
eis 2714690 p.Phe215Leu missense_variant 0.33
eis 2714829 c.504C>A synonymous_variant 0.2
eis 2714839 p.Leu165Ser missense_variant 0.2
ahpC 2726167 c.-26T>G upstream_gene_variant 0.2
ahpC 2726388 p.Ala66Pro missense_variant 0.13
ahpC 2726436 p.Ile82Val missense_variant 0.13
folC 2746491 p.Phe370Leu missense_variant 0.18
folC 2747775 c.-177C>T upstream_gene_variant 0.2
pepQ 2859738 c.681C>T synonymous_variant 0.22
pepQ 2859797 p.Thr208Ser missense_variant 0.18
pepQ 2860485 c.-67C>T upstream_gene_variant 0.33
ribD 2986936 c.100_104dupTATCC frameshift_variant 0.33
ribD 2987574 p.Asp246Tyr missense_variant 0.2
Rv2752c 3064602 c.1590T>C synonymous_variant 0.29
Rv2752c 3065036 p.Asn386His missense_variant 0.5
thyX 3067801 p.Lys49Glu missense_variant 0.4
thyX 3068043 c.-98A>G upstream_gene_variant 0.25
thyA 3073756 p.Phe239Ser missense_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087015 c.198delC frameshift_variant 0.5
ald 3087728 c.909C>A synonymous_variant 0.12
Rv3083 3448422 c.-82T>C upstream_gene_variant 0.22
Rv3083 3448471 c.-33T>C upstream_gene_variant 0.2
Rv3083 3448840 p.Gln113Glu missense_variant 0.33
fprA 3473928 c.-79T>G upstream_gene_variant 0.22
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474048 c.42G>A synonymous_variant 0.5
fprA 3474961 p.Val319Leu missense_variant 1.0
whiB7 3568704 c.-28_-26delCCA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612816 p.Ala101Thr missense_variant 0.29
fbiA 3640810 c.269delA frameshift_variant 0.25
fbiA 3641470 p.Met310Val missense_variant 1.0
fbiB 3641718 p.Pro62Ser missense_variant 0.25
fbiB 3641977 p.Ile148Thr missense_variant 0.22
alr 3840357 p.Leu355Pro missense_variant 0.29
alr 3841116 p.Ala102Val missense_variant 0.4
rpoA 3877804 p.Gly235Val missense_variant 0.33
rpoA 3878278 p.Ile77Thr missense_variant 0.22
rpoA 3878411 p.Thr33Ala missense_variant 0.2
clpC1 4038512 c.2193C>A synonymous_variant 0.22
clpC1 4038954 p.Glu584Gly missense_variant 0.25
clpC1 4039625 p.Lys360Asn missense_variant 0.25
clpC1 4040396 c.309C>T synonymous_variant 0.15
panD 4043998 p.Asp95Gly missense_variant 0.5
embC 4239774 c.-89C>A upstream_gene_variant 0.33
embC 4239880 c.18C>T synonymous_variant 0.33
embC 4240470 p.Asp203Gly missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242868 c.-365C>A upstream_gene_variant 0.33
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244414 c.1182G>C synonymous_variant 1.0
embA 4244689 p.Lys486Arg missense_variant 0.18
embA 4244746 p.Leu505Pro missense_variant 0.4
embA 4246392 c.3164delG frameshift_variant 0.25
embB 4247817 p.Val435Ala missense_variant 0.25
embB 4248395 p.Phe628Leu missense_variant 0.22
embB 4248434 p.Ala641Ser missense_variant 0.18
embB 4249548 p.Phe1012Ser missense_variant 0.29
aftB 4267500 p.Pro446Leu missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268143 p.Tyr232His missense_variant 0.25
aftB 4268291 p.Ser182Arg missense_variant 0.2
ethA 4326216 p.Glu420* stop_gained 0.17
ethA 4326345 p.Ile377Val missense_variant 0.15
ethA 4326404 p.Asp357Gly missense_variant 0.14
ethA 4326441 p.Asn345His missense_variant 0.12
ethA 4326498 c.976C>A synonymous_variant 0.12
ethA 4326552 p.Gly308Trp missense_variant 0.18
ethA 4326720 p.Ala252Pro missense_variant 0.33
ethR 4326778 c.-771G>A upstream_gene_variant 0.2
ethA 4326840 p.Ile212Val missense_variant 0.14
ethA 4327062 p.Ser138Arg missense_variant 0.22
ethA 4327158 p.Ser106Gly missense_variant 0.13
ethA 4328206 c.-734delA upstream_gene_variant 0.22
whiB6 4338473 c.49A>C synonymous_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338668 c.-148delC upstream_gene_variant 0.14
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407603 c.600G>A synonymous_variant 0.33
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407762 p.Lys147Asn missense_variant 0.33
gid 4407870 c.333C>T synonymous_variant 0.22
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408440 c.-238C>G upstream_gene_variant 0.5