TB-Profiler result

Run: ERR5866537
Summary

Run ID: ERR5866537

Sample name:

Date: 02-04-2023 00:45:08

Number of reads: 696310

Percentage reads mapped: 99.47

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 East-Asian Beijing RD105 1.0
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 0.9 isoniazid, ethionamide
folC 2747151 p.Ser150Gly missense_variant 1.0 para-aminosalicylic_acid
embB 4247574 p.Asp354Ala missense_variant 1.0 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7875 p.His192Asn missense_variant 0.14
gyrA 9071 c.1770G>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491169 p.Phe129Leu missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575419 c.72C>A synonymous_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576519 p.Ser391Tyr missense_variant 0.17
mshA 576640 p.Glu431Asp missense_variant 0.22
mshA 576773 p.Arg476Ser missense_variant 0.22
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761006 c.1200C>A synonymous_variant 0.22
rpoB 761536 p.Pro577His missense_variant 0.22
rpoB 762184 p.Gly793Val missense_variant 0.18
rpoB 762732 p.Glu976* stop_gained 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764794 p.Met475Ile missense_variant 0.18
rpoC 765461 p.Asn698His missense_variant 1.0
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766928 p.Glu1187* stop_gained 0.29
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 776777 c.1704C>A synonymous_variant 0.14
mmpL5 777049 c.1431dupG frameshift_variant 0.2
mmpL5 777659 c.822C>A synonymous_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801084 c.276G>T synonymous_variant 0.25
fbiC 1302937 p.Gln3Lys missense_variant 0.18
fbiC 1303138 c.209delT frameshift_variant 0.17
fbiC 1303672 p.Ala248Ser missense_variant 0.22
fbiC 1305092 p.Ala721Asp missense_variant 0.18
fbiC 1305422 p.Ala831Asp missense_variant 0.15
Rv1258c 1406241 c.1098_1099delGG frameshift_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407501 c.-161C>A upstream_gene_variant 0.18
embR 1417308 p.Gly14Cys missense_variant 0.22
embR 1417314 p.Asp12Tyr missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474297 n.640C>A non_coding_transcript_exon_variant 0.67
inhA 1673676 c.-526G>T upstream_gene_variant 0.17
inhA 1674162 c.-40C>A upstream_gene_variant 0.2
rpsA 1833650 p.Asp37Tyr missense_variant 0.25
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102005 c.1038G>T synonymous_variant 0.18
ndh 2102073 p.Ala324Ser missense_variant 0.18
ndh 2102571 p.Ala158Ser missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155787 p.Ala109Thr missense_variant 1.0
katG 2155974 p.Lys46Asn missense_variant 0.25
katG 2156159 c.-48C>A upstream_gene_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168155 p.Thr820Ser missense_variant 0.17
PPE35 2168179 p.Pro812Thr missense_variant 0.18
PPE35 2168206 p.Pro803Thr missense_variant 0.17
PPE35 2170253 c.360G>T synonymous_variant 0.18
PPE35 2170355 c.258G>T synonymous_variant 0.22
Rv1979c 2222062 p.Arg368Leu missense_variant 0.25
Rv1979c 2222519 p.Gly216Cys missense_variant 0.17
Rv1979c 2222630 p.Val179Phe missense_variant 0.15
Rv1979c 2222660 p.Gly169Cys missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289191 c.51C>A synonymous_variant 0.18
pncA 2289211 c.22_30delGACGTGCAG conservative_inframe_deletion 1.0
pncA 2289549 c.-308G>T upstream_gene_variant 0.15
pncA 2289643 c.-402C>A upstream_gene_variant 0.2
pncA 2289691 c.-450G>T upstream_gene_variant 0.18
ahpC 2725959 c.-234C>A upstream_gene_variant 0.15
ahpC 2726073 c.-120C>A upstream_gene_variant 0.12
folC 2746565 p.Ala345Glu missense_variant 0.29
folC 2746660 p.Phe313Leu missense_variant 0.22
ribD 2986676 c.-163C>A upstream_gene_variant 0.29
ribD 2986679 c.-160G>T upstream_gene_variant 0.33
ribD 2986923 p.Pro29Thr missense_variant 0.29
Rv2752c 3064820 p.Gly458Cys missense_variant 0.33
Rv2752c 3065118 c.1074C>A synonymous_variant 0.29
thyA 3073681 c.791G>T stop_lost&splice_region_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339181 p.Ala22Ser missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474435 c.429C>A synonymous_variant 0.17
Rv3236c 3612270 p.Asp283Tyr missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613033 p.Phe28Leu missense_variant 0.38
alr 3840974 c.447C>A synonymous_variant 0.18
alr 3841351 p.Ala24Thr missense_variant 0.15
clpC1 4038511 p.Asp732Asn missense_variant 0.18
clpC1 4040798 c.-94G>T upstream_gene_variant 0.15
embC 4240018 c.156C>A synonymous_variant 0.2
embC 4240298 p.Gln146Lys missense_variant 0.22
embC 4240868 p.His336Asn missense_variant 0.2
embC 4241314 c.1452G>T synonymous_variant 0.18
embC 4241807 p.Pro649Thr missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242778 p.Gln972His missense_variant 0.15
embC 4242938 p.Asp1026Tyr missense_variant 0.2
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244304 c.1072C>A synonymous_variant 0.2
embA 4245942 p.Arg904Gly missense_variant 0.2
embA 4246309 p.Thr1026Asn missense_variant 0.12
embB 4246921 c.408G>A synonymous_variant 0.22
aftB 4267532 p.Met435Ile missense_variant 0.22
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327074 p.Leu134Ile missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407881 p.Leu108Met missense_variant 0.29
gid 4407927 p.Glu92Asp missense_variant 1.0