TB-Profiler result

Run: SRR22175191
Summary

Run ID: SRR22175191

Sample name:

Date: 04-04-2023 04:00:08

Number of reads: 583458

Percentage reads mapped: 99.32

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 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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.Asp94Tyr missense_variant 0.93 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289228 p.Ile5Ser missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.96 kanamycin
thyA 3074408 p.Thr22Ala missense_variant 0.94 para-aminosalicylic_acid
embA 4243217 c.-16C>T upstream_gene_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
gyrB 5642 p.Leu135Phe missense_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7427 c.126G>A synonymous_variant 0.15
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8276 c.975G>A synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491290 p.Val170Met missense_variant 1.0
fgd1 491395 p.Glu205Lys missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575191 c.-157C>T upstream_gene_variant 0.12
mshA 575440 c.93C>T synonymous_variant 0.13
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761304 p.Val500Ile missense_variant 0.18
rpoB 762123 p.Glu773Lys missense_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
rpoC 763504 c.135C>A synonymous_variant 0.12
rpoC 764384 p.Asp339Tyr missense_variant 0.14
rpoC 766415 p.His1016Asn missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.89
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777889 p.Gln198* stop_gained 0.15
mmpL5 778753 c.-273C>T upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800663 c.-146G>T upstream_gene_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 0.86
embR 1416250 c.1098C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472981 n.1136G>A non_coding_transcript_exon_variant 0.13
rrs 1473055 n.1210C>A non_coding_transcript_exon_variant 0.13
rrl 1473847 n.190G>A non_coding_transcript_exon_variant 0.11
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 1.0
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 2223243 c.-79G>A upstream_gene_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714261 p.Ser358Gly missense_variant 0.12
Rv2752c 3064914 c.1278T>C synonymous_variant 0.2
Rv2752c 3064950 c.1242C>T synonymous_variant 0.2
thyX 3067949 c.-4C>T upstream_gene_variant 1.0
thyX 3068102 c.-157T>C upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448409 c.-95G>A upstream_gene_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474218 p.Ala71Val missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 0.83
embC 4241022 p.Ala387Val missense_variant 0.96
embC 4242284 p.Phe808Leu missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embB 4247847 p.Gln445Arg missense_variant 1.0
embB 4248585 p.Arg691His missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338292 p.Ala77Val missense_variant 0.9
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.86
gid 4407620 p.Tyr195His missense_variant 0.8
gid 4407927 p.Glu92Asp missense_variant 1.0