TB-Profiler result

Run: ERR7801248
Summary

Run ID: ERR7801248

Sample name:

Date: 02-04-2023 06:00:17

Number of reads: 580288

Percentage reads mapped: 99.45

Strain: lineage4.3.4.2

Drug-resistance: Other

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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 0.98
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.99
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
embB 4247579 p.Ala356Ser missense_variant 0.17 ethambutol
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 8654 c.1353C>A synonymous_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9509 c.2208G>A synonymous_variant 0.17
fgd1 491001 c.219G>A synonymous_variant 0.13
fgd1 491018 p.Phe79Ser missense_variant 0.17
mshA 576505 c.1158C>T synonymous_variant 0.17
ccsA 620371 p.Ala161Thr missense_variant 0.33
ccsA 620568 c.678C>T synonymous_variant 0.14
rpoB 759958 p.Gln51Arg missense_variant 0.1
rpoB 761863 p.Ala686Glu missense_variant 0.14
rpoB 762167 c.2361T>C synonymous_variant 0.17
rpoB 763156 p.Val1117Ala missense_variant 0.1
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765280 c.1911G>A synonymous_variant 0.17
rpoC 765529 c.2160C>A synonymous_variant 0.18
rpoC 766138 c.2769G>T synonymous_variant 0.15
rpoC 766313 p.Ser982Thr missense_variant 0.23
mmpL5 775616 c.2865G>A synonymous_variant 0.18
mmpL5 775620 p.Ser954* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776070 p.Ile804Thr missense_variant 0.15
mmpL5 777021 p.Pro487Leu missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801262 p.Gly152Cys missense_variant 0.17
fbiC 1305357 c.2427C>A synonymous_variant 0.12
Rv1258c 1406353 p.Pro330Thr missense_variant 0.18
Rv1258c 1406841 p.Thr167Met missense_variant 0.14
Rv1258c 1407515 c.-175G>T upstream_gene_variant 0.13
embR 1416989 c.358delA frameshift_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473785 n.128C>T non_coding_transcript_exon_variant 0.17
rrl 1474150 n.493C>A non_coding_transcript_exon_variant 0.15
inhA 1674639 c.438C>T synonymous_variant 0.15
rpsA 1833766 c.225C>T synonymous_variant 0.13
rpsA 1834355 p.Val272Ile missense_variant 0.13
tlyA 1917886 c.-54C>G upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102200 c.843G>T synonymous_variant 0.14
katG 2154716 p.Gly466* stop_gained 0.18
katG 2155029 c.1083C>T synonymous_variant 0.22
katG 2155397 p.Pro239Thr missense_variant 0.15
PPE35 2169833 c.780A>G synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.21
Rv1979c 2222375 p.Gly264Cys missense_variant 0.18
Rv1979c 2222905 p.Gly87Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289909 c.-668G>A upstream_gene_variant 0.17
kasA 2518166 p.Ala18Thr missense_variant 0.17
kasA 2518825 p.Phe237Leu missense_variant 0.14
eis 2714560 p.Gly258Val missense_variant 0.18
eis 2714983 p.Ala117Glu missense_variant 0.18
folC 2746359 p.Val414Ile missense_variant 0.33
folC 2746444 p.Lys385Asn missense_variant 0.33
folC 2746824 p.Glu259* stop_gained 0.13
pepQ 2859741 c.678C>A synonymous_variant 0.15
pepQ 2860226 p.Ala65Ser missense_variant 0.14
Rv2752c 3065251 p.Ala314Glu missense_variant 0.14
Rv2752c 3066134 p.Ala20Thr missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448944 c.441G>T synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568523 c.157T>C synonymous_variant 0.13
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3640792 p.Glu84Lys missense_variant 0.18
fbiA 3641521 p.Ala327Thr missense_variant 0.15
fbiB 3641564 c.30G>T synonymous_variant 0.14
fbiB 3642017 c.483C>T synonymous_variant 0.17
fbiB 3642381 p.Ala283Ser missense_variant 0.13
ddn 3987221 p.Leu126Phe missense_variant 0.16
clpC1 4038220 p.Glu829* stop_gained 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038680 p.Lys675Asn missense_variant 0.12
clpC1 4039973 p.Asp244Glu missense_variant 0.18
clpC1 4040637 p.Leu23Arg missense_variant 0.12
panD 4044183 p.Met33Ile missense_variant 0.14
panD 4044201 c.81C>G synonymous_variant 0.14
embC 4240116 p.Thr85Asn missense_variant 0.13
embC 4242363 p.Gly834Val missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243913 c.681C>A synonymous_variant 0.14
embA 4244371 p.Arg380Leu missense_variant 0.13
embA 4244722 p.Gln497Leu missense_variant 0.14
embA 4244869 p.Ser546Ile missense_variant 0.14
embA 4245540 p.Val770Ile missense_variant 0.18
embA 4245770 p.Asn846Lys missense_variant 0.17
embA 4245850 p.Ala873Val missense_variant 0.15
embA 4246044 p.Val938Leu missense_variant 0.13
embB 4247795 p.Leu428Ile missense_variant 0.12
embB 4248937 p.Gln808His missense_variant 0.15
embB 4249098 p.Trp862Leu missense_variant 0.2
aftB 4267560 p.Ala426Asp missense_variant 0.15
aftB 4267977 p.Pro287Gln missense_variant 0.2
ethA 4326864 p.Met204Leu missense_variant 0.12
ethA 4328019 c.-546G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0