TB-Profiler result

Run: SRR3082103
Summary

Run ID: SRR3082103

Sample name:

Date: 04-04-2023 04:53:44

Number of reads: 582830

Percentage reads mapped: 98.75

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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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
pncA 2288764 p.Thr160Ala missense_variant 1.0 pyrazinamide
pncA 2288781 p.Arg154Met missense_variant 1.0 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 762226 p.Glu807Gly missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763699 c.330G>A synonymous_variant 0.12
rpoC 764673 p.Gln435Arg missense_variant 0.18
rpoC 764723 p.Phe452Leu missense_variant 1.0
rpoC 767198 p.Glu1277Gln missense_variant 0.12
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
fbiC 1303144 p.Ser72Pro missense_variant 0.15
fbiC 1304684 p.Ala585Val missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473199 n.1354C>T non_coding_transcript_exon_variant 0.13
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.11
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.11
rrl 1476326 n.2673delA non_coding_transcript_exon_variant 0.13
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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746347 p.Ala418Thr missense_variant 0.12
Rv2752c 3064780 p.Gly471Asp missense_variant 1.0
thyA 3073839 c.633T>C synonymous_variant 0.17
thyA 3073860 c.612C>G synonymous_variant 0.29
thyA 3073863 c.609T>C synonymous_variant 0.18
thyA 3073866 c.606C>G synonymous_variant 0.18
thyA 3073872 p.Ile200Val missense_variant 0.15
thyA 3073890 c.580_582delTTGinsCTA synonymous_variant 0.13
thyA 3073898 p.Ala192Ser missense_variant 0.12
thyA 3074449 p.Leu8Pro missense_variant 0.14
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4039966 p.Leu247Ile missense_variant 0.12
clpC1 4040042 c.663C>A synonymous_variant 0.14
embC 4240201 c.339G>T synonymous_variant 0.29
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 4249567 p.Tyr1018* stop_gained 0.2
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 1.0