TB-Profiler result

Run: SRR1173393
Summary

Run ID: SRR1173393

Sample name:

Date: 03-04-2023 03:24:33

Number of reads: 6369069

Percentage reads mapped: 98.69

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 0.99
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 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.95 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.38 isoniazid, ethionamide
inhA 1674048 c.-154G>A upstream_gene_variant 0.43 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2289222 p.Val7Gly missense_variant 0.94 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326707 p.Trp256* stop_gained 0.98 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 7362 p.Glu21Gln missense_variant 1.0
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 575874 p.Thr176Ile missense_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619749 c.-142T>G upstream_gene_variant 0.22
ccsA 620302 p.Trp138Arg missense_variant 0.13
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 766390 c.3021C>G synonymous_variant 0.1
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 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 0.99
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168059 p.Gln852Lys missense_variant 0.11
PPE35 2169320 p.Leu431Phe missense_variant 0.34
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714739 c.594C>T synonymous_variant 0.11
thyX 3067570 p.Ala126Thr missense_variant 0.11
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087459 c.640_641insT frameshift_variant 0.14
ald 3087897 p.Gly360Arg missense_variant 0.29
fbiD 3338979 c.-139G>T upstream_gene_variant 0.14
fbiD 3339023 c.-95G>T upstream_gene_variant 0.13
Rv3083 3448887 c.384C>A synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840475 p.Asp316Tyr missense_variant 0.21
clpC1 4038857 c.1848C>A synonymous_variant 0.23
clpC1 4040228 c.477G>A synonymous_variant 0.18
embC 4240587 p.Gly242Val missense_variant 0.14
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 4247620 c.1107G>T synonymous_variant 0.14
embB 4248848 p.Pro779Ala missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
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 0.97