TB-Profiler result

Run: ERR4799883
Summary

Run ID: ERR4799883

Sample name:

Date: 01-04-2023 09:26:20

Number of reads: 3336817

Percentage reads mapped: 99.28

Strain: lineage1.2.2.2

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
lineage1 Indo-Oceanic EAI RD239 0.97
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.98
lineage1.2.2.2 Indo-Oceanic NA RD239 0.97
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 7570 p.Ala90Val missense_variant 0.43 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.27 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 0.92 isoniazid, ethionamide
inhA 1674481 p.Ser94Ala missense_variant 0.98 isoniazid, ethionamide
pncA 2289091 p.His51Tyr missense_variant 0.94 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.97 kanamycin
embB 4247730 p.Gly406Asp missense_variant 0.94 ethambutol
gid 4407816 c.386delG frameshift_variant 0.96 streptomycin
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 5075 c.-165C>T upstream_gene_variant 0.92
gyrB 6112 p.Met291Ile missense_variant 0.97
gyrA 7268 c.-34C>T upstream_gene_variant 0.96
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8164 p.Ala288Asp missense_variant 0.18
gyrA 8452 p.Ala384Val missense_variant 0.99
gyrA 8513 c.1212C>A synonymous_variant 0.96
gyrA 9143 c.1842T>C synonymous_variant 0.93
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 0.99
rpoC 763884 p.Ala172Val missense_variant 0.98
rpoC 763886 c.517C>A synonymous_variant 0.96
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 776100 p.Thr794Ile missense_variant 0.99
mmpL5 777431 c.1047_1049delCGC disruptive_inframe_deletion 0.93
mmpS5 779625 c.-720G>A upstream_gene_variant 0.95
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.94
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102240 p.Arg268His missense_variant 0.96
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 0.95
Rv1979c 2222308 p.Asp286Gly missense_variant 0.97
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288724 p.Glu173Gly missense_variant 0.94
kasA 2518132 c.18C>T synonymous_variant 1.0
ahpC 2726051 c.-142G>A upstream_gene_variant 0.99
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.94
fprA 3475159 p.Asn385Asp missense_variant 1.0
clpC1 4040517 p.Val63Ala missense_variant 0.96
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 0.97
aftB 4267960 p.Val293Met missense_variant 0.97
ubiA 4269387 p.Glu149Asp missense_variant 0.95
aftB 4269606 c.-770T>C upstream_gene_variant 0.92
ethA 4326148 c.1326G>T synonymous_variant 0.98
ethA 4326439 p.Asn345Lys missense_variant 0.98
whiB6 4338203 p.Arg107Cys missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407848 p.Ala119Thr missense_variant 0.96
gid 4407873 c.330G>T synonymous_variant 0.93