TB-Profiler result

Run: ERR8665529
Summary

Run ID: ERR8665529

Sample name:

Date: 02-04-2023 07:30:53

Number of reads: 949008

Percentage reads mapped: 99.58

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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
gyrA 7572 p.Ser91Pro missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289040 p.Trp68Gly missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326087 c.1386delA 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
gyrA 6478 c.-824G>T upstream_gene_variant 0.18
gyrA 7250 c.-52C>A upstream_gene_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7507 p.Ser69Ile missense_variant 0.19
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576491 p.Arg382Cys missense_variant 0.15
mshA 576592 c.1245G>T synonymous_variant 0.14
ccsA 620086 p.Asp66Tyr missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760760 c.954C>A synonymous_variant 0.19
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763906 c.537C>A synonymous_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778506 p.Leu134Met missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834964 p.Glu475* stop_gained 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154968 p.Leu382Ile missense_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170431 p.Ser61* stop_gained 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2725918 c.-275G>T upstream_gene_variant 0.4
folC 2747596 c.3G>T start_lost 0.18
ribD 2986646 c.-193G>T upstream_gene_variant 0.17
Rv2752c 3065008 p.Pro395Gln missense_variant 0.19
Rv2752c 3065345 p.Asp283Tyr missense_variant 0.25
thyX 3067560 p.Arg129Pro missense_variant 0.17
thyA 3074321 p.His51Asn missense_variant 0.2
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087452 p.Phe211Leu missense_variant 0.17
Rv3083 3449023 p.Asp174Tyr missense_variant 0.18
Rv3083 3449207 p.Pro235Gln missense_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568795 c.-116A>G upstream_gene_variant 1.0
Rv3236c 3612067 c.1050G>T synonymous_variant 0.14
Rv3236c 3612498 p.Gly207Cys missense_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3612835 c.282T>G synonymous_variant 0.18
fbiA 3641354 p.Ala271Asp missense_variant 0.13
fbiB 3642853 p.Pro440His missense_variant 0.2
clpC1 4038316 p.Gly797Cys missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247261 p.Gln250Lys missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267970 p.Phe289Leu missense_variant 0.17
aftB 4268876 c.-40G>T upstream_gene_variant 0.2
ethA 4327965 c.-492C>A upstream_gene_variant 0.21
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0