TB-Profiler result

Run: ERR5866523
Summary

Run ID: ERR5866523

Sample name:

Date: 02-04-2023 00:44:23

Number of reads: 445864

Percentage reads mapped: 99.54

Strain: lineage2.2.1

Drug-resistance: MDR-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
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
katG 2155341 c.770delT frameshift_variant 0.4 isoniazid
katG 2155791 p.Trp107* stop_gained 0.29 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326231 c.1242delT frameshift_variant 1.0 ethionamide, 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 5405 p.Glu56* stop_gained 0.25
gyrB 6191 p.Glu318* stop_gained 0.29
gyrB 6322 p.Lys361Asn missense_variant 0.4
gyrB 6575 p.Arg446Ser missense_variant 0.22
gyrB 6719 p.Asp494Tyr missense_variant 0.25
gyrB 7169 p.Ala644Thr missense_variant 0.67
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7712 p.Leu137Phe missense_variant 0.22
gyrA 8586 p.Glu429* stop_gained 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9762 p.Glu821* stop_gained 0.14
fgd1 490589 c.-194G>T upstream_gene_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575284 c.-64C>T upstream_gene_variant 0.17
mshA 575591 p.Arg82Trp missense_variant 0.21
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576520 c.1176delG frameshift_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760451 c.645C>T synonymous_variant 0.33
rpoB 760517 p.Trp237Cys missense_variant 0.33
rpoB 760663 p.Ala286Glu missense_variant 0.5
rpoB 761525 p.Met573Ile missense_variant 0.15
rpoB 761714 c.1908C>A synonymous_variant 0.18
rpoB 761733 p.Val643Ile missense_variant 0.2
rpoB 761749 p.Ser648* stop_gained 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763103 c.-267G>T upstream_gene_variant 0.33
rpoC 764813 p.Gln482Lys missense_variant 0.29
rpoC 764822 p.Asp485Tyr missense_variant 1.0
rpoC 766144 c.2775G>A synonymous_variant 0.29
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766899 p.Pro1177His missense_variant 0.29
rpoC 767128 c.3759C>T synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775754 c.2727C>A synonymous_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpR5 778178 c.-812G>A upstream_gene_variant 0.15
mmpR5 778346 c.-644G>T upstream_gene_variant 0.33
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801101 p.Gly98Val missense_variant 0.29
fbiC 1303010 p.Arg27Leu missense_variant 0.17
fbiC 1305009 c.2079C>A synonymous_variant 0.33
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406885 c.456G>T synonymous_variant 0.2
Rv1258c 1407022 p.Ala107Ser missense_variant 0.14
Rv1258c 1407492 c.-152C>A upstream_gene_variant 0.13
embR 1416778 c.570G>T synonymous_variant 0.18
embR 1417249 c.99C>A synonymous_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476733 n.3076C>A non_coding_transcript_exon_variant 0.67
fabG1 1673151 c.-289C>A upstream_gene_variant 0.17
fabG1 1674137 p.Ser233Tyr missense_variant 0.33
rpsA 1833959 p.Leu140Ile missense_variant 0.33
rpsA 1834118 p.Gln193Lys missense_variant 0.33
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918734 p.Ser265Arg missense_variant 0.5
ndh 2103040 c.3G>T start_lost 0.5
ndh 2103113 c.-71C>T upstream_gene_variant 0.29
katG 2153969 p.Asp715Tyr missense_variant 0.18
katG 2154051 c.2061G>T synonymous_variant 0.2
katG 2154238 p.Thr625Lys missense_variant 0.4
katG 2154703 p.Ser470* stop_gained 0.67
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156012 p.Gly34* stop_gained 0.29
PPE35 2167708 p.Gly969Cys missense_variant 0.29
PPE35 2168442 p.Trp724Leu missense_variant 0.18
PPE35 2168545 p.Gly690Trp missense_variant 0.67
PPE35 2170704 c.-92C>A upstream_gene_variant 0.2
PPE35 2170707 c.-95G>T upstream_gene_variant 0.18
Rv1979c 2221747 p.Arg473Leu missense_variant 0.33
Rv1979c 2222809 p.Arg119Leu missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289933 c.-692G>T upstream_gene_variant 0.4
eis 2715278 p.Leu19Met missense_variant 0.17
eis 2715411 c.-79A>G upstream_gene_variant 0.15
ribD 2987200 p.Thr121Asn missense_variant 0.18
Rv2752c 3064699 p.Ser498Tyr missense_variant 0.67
Rv2752c 3065729 p.Ala155Thr missense_variant 0.25
Rv2752c 3066303 c.-112C>A upstream_gene_variant 0.33
thyA 3073701 c.771C>A synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087341 c.522C>A synonymous_variant 0.18
ald 3087820 p.Arg334Leu missense_variant 0.2
fbiD 3339435 c.318G>T synonymous_variant 0.13
Rv3083 3448656 c.153G>A synonymous_variant 0.18
fprA 3474928 p.Gly308Cys missense_variant 0.17
fprA 3475113 c.1107G>T synonymous_variant 0.17
whiB7 3568572 c.108C>A synonymous_variant 0.25
Rv3236c 3612469 p.Glu216Asp missense_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641230 p.Arg230Ser missense_variant 0.22
fbiB 3641640 p.Ala36* stop_gained 0.15
ddn 3986982 p.Ala47Thr missense_variant 0.33
clpC1 4040109 p.Arg199Gln missense_variant 0.29
clpC1 4040301 p.Arg135His missense_variant 0.25
clpC1 4040507 c.198C>A synonymous_variant 0.17
panD 4044259 p.Ser8* stop_gained 0.2
embC 4240737 p.Ser292Tyr missense_variant 0.15
embC 4241035 c.1173G>T synonymous_variant 0.18
embC 4241397 p.Trp512Leu missense_variant 0.22
embC 4241457 p.Ala532Asp missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242750 p.Pro963Gln missense_variant 0.18
embA 4243299 p.Ala23Ser missense_variant 0.29
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244068 p.Thr279Ile missense_variant 0.18
embA 4245091 p.Gly620Val missense_variant 0.22
embB 4246181 c.-333C>A upstream_gene_variant 0.14
embB 4248883 c.2370C>A synonymous_variant 0.2
embB 4249452 p.Ser980* stop_gained 0.2
embB 4249495 p.Phe994Leu missense_variant 0.25
embB 4249543 c.3030G>A synonymous_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268273 c.564A>G synonymous_variant 0.18
aftB 4268746 p.Gly31Arg missense_variant 0.25
ubiA 4269896 c.-63G>A upstream_gene_variant 0.13
ethA 4326033 p.Ala481Thr missense_variant 0.22
ethA 4326099 p.Gln459Lys missense_variant 0.25
ethA 4326333 p.Ala381Ser missense_variant 0.33
ethR 4326670 c.-879G>T upstream_gene_variant 0.5
ethA 4327671 c.-198C>A upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407810 c.393C>T synonymous_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 0.67