TB-Profiler result

Run: SRR1172895
Summary

Run ID: SRR1172895

Sample name:

Date: 03-04-2023 03:12:54

Number of reads: 5202426

Percentage reads mapped: 74.63

Strain: lineage3.1.3;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
lineage3 East-African-Indian CAS RD750 0.9
lineage2 East-Asian Beijing RD105 0.08
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.06
lineage3.1.3 East-African-Indian CAS RD750 0.89
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.05
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.Asp94Ala missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.93 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.13 streptomycin
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 0.91 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289231 p.Leu4Ser missense_variant 0.48 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.13 kanamycin
embA 4243217 c.-16C>T upstream_gene_variant 0.2 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.89 ethambutol
pncA 2285167 c.17_*3513del frameshift_variant&stop_lost&splice_region_variant 1.0 pyrazinamide
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 0.13
rpoC 762434 c.-936T>G upstream_gene_variant 0.91
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801130 p.Asp108His missense_variant 0.93
Rv1258c 1406760 c.580_581insC frameshift_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834159 c.618G>A synonymous_variant 0.91
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 2168789 c.1824C>T synonymous_variant 0.89
Rv1979c 2222732 c.432delT frameshift_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.9
ahpC 2726105 c.-88G>A upstream_gene_variant 0.87
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641038 p.Ala166Ser missense_variant 0.86
clpC1 4039066 p.Gly547Ser missense_variant 0.84
embC 4242075 p.Arg738Gln missense_variant 0.87
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.19
embB 4248254 p.Thr581Ala missense_variant 0.13
embB 4249195 c.2682C>A synonymous_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.12
gid 4408175 p.Ala10Pro missense_variant 0.94