TB-Profiler result

Run: ERR2515492
Summary

Run ID: ERR2515492

Sample name:

Date: 31-03-2023 20:58:02

Number of reads: 585510

Percentage reads mapped: 99.77

Strain: lineage4.3.4.2.1

Drug-resistance: Sensitive

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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 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
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 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8784 p.Arg495Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491391 c.609C>T synonymous_variant 0.14
mshA 576067 c.720C>T synonymous_variant 0.15
ccsA 619696 c.-195C>G upstream_gene_variant 0.25
ccsA 619759 c.-131delG upstream_gene_variant 0.29
rpoB 760781 c.975G>A synonymous_variant 0.18
rpoC 763693 c.324G>A synonymous_variant 0.11
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766393 c.3024C>T synonymous_variant 1.0
mmpL5 775592 c.2889G>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776238 p.Gly748Asp missense_variant 0.11
mmpL5 776309 c.2172C>T synonymous_variant 0.16
mmpL5 776608 p.Gln625* stop_gained 0.15
mmpL5 776882 c.1599C>T synonymous_variant 0.15
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781542 c.-18A>T upstream_gene_variant 0.12
rplC 801298 p.Thr164Ala missense_variant 0.11
Rv1258c 1406562 p.Leu260Pro missense_variant 0.14
Rv1258c 1407283 p.Ala20Thr missense_variant 0.15
Rv1258c 1407296 c.44delC frameshift_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475167 n.1510T>G non_coding_transcript_exon_variant 0.2
rrl 1476155 n.2498C>G non_coding_transcript_exon_variant 0.12
rrl 1476781 n.3124C>T non_coding_transcript_exon_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101879 c.1164C>T synonymous_variant 0.11
ndh 2102285 p.Asp253Val missense_variant 0.11
katG 2154418 p.Val565Glu missense_variant 0.12
katG 2155404 p.Asn236Lys missense_variant 0.15
katG 2155975 p.Lys46Met missense_variant 0.11
PPE35 2167769 c.2844C>T synonymous_variant 0.12
PPE35 2168820 p.Ala598Gly missense_variant 0.25
PPE35 2169678 p.Leu312Pro missense_variant 0.12
PPE35 2170576 p.Ala13Pro missense_variant 0.12
Rv1979c 2222783 p.Ala128Pro missense_variant 0.11
Rv1979c 2222994 c.170delT frameshift_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289549 c.-308G>T upstream_gene_variant 0.18
kasA 2518089 c.-26C>A upstream_gene_variant 0.11
kasA 2518712 p.Gly200* stop_gained 0.2
kasA 2518829 p.Phe239Ile missense_variant 0.18
folC 2746210 c.1389A>G synonymous_variant 0.13
folC 2747285 p.Val105Ala missense_variant 0.1
pepQ 2860261 p.Val53Ala missense_variant 0.12
ribD 2986676 c.-163C>T upstream_gene_variant 0.1
ribD 2987490 p.Tyr218Asn missense_variant 0.11
Rv2752c 3066292 c.-101A>G upstream_gene_variant 0.12
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086783 c.-37C>A upstream_gene_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087756 c.937C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474173 p.Asp56Gly missense_variant 0.1
fprA 3474809 p.Val268Glu missense_variant 0.15
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3613036 c.81A>G synonymous_variant 0.18
fbiA 3640927 p.Thr129Ser missense_variant 0.11
alr 3840719 c.702A>G synonymous_variant 1.0
rpoA 3878488 p.Pro7Leu missense_variant 0.17
ddn 3986693 c.-150delG upstream_gene_variant 0.11
ddn 3987237 p.Ser132Gly missense_variant 0.12
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4240630 c.768C>T synonymous_variant 0.12
embC 4241146 c.1284C>A synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244952 p.Phe574Leu missense_variant 0.12
embA 4245450 p.Leu740Met missense_variant 0.1
aftB 4267671 c.1165delG frameshift_variant 0.11
aftB 4267740 p.Glu366Gly missense_variant 0.14
aftB 4268888 c.-52C>G upstream_gene_variant 0.14
aftB 4269237 c.-401C>T upstream_gene_variant 0.15
ethA 4327938 c.-465G>T upstream_gene_variant 0.12
ethR 4328120 p.Gln191Arg missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0