TB-Profiler result

Run: SRR3105745
Summary

Run ID: SRR3105745

Sample name:

Date: 04-04-2023 05:08:00

Number of reads: 4804956

Percentage reads mapped: 97.74

Strain: lineage4;lineage3

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 0.92
lineage4 Euro-American LAM;T;S;X;H None 0.08
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 0.8 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 0.93 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.11 isoniazid
embB 4247730 p.Gly406Asp missense_variant 0.96 ethambutol
gid 4408100 c.102delG frameshift_variant 0.91 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
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 0.92
rpoB 759746 c.-61C>T upstream_gene_variant 0.9
rpoB 760719 p.Val305Ile missense_variant 0.63
rpoB 761850 p.Pro682Ala missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 0.9
rpoC 763031 c.-339T>C upstream_gene_variant 0.84
rpoC 767314 p.Tyr1315* stop_gained 0.38
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.88
mmpL5 777320 c.1161C>G synonymous_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833742 p.Glu67Asp missense_variant 0.93
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.96
katG 2155216 p.Gly299Val missense_variant 0.91
PPE35 2167926 p.Leu896Ser missense_variant 0.9
PPE35 2168087 c.2526G>A synonymous_variant 0.93
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.92
ahpC 2726105 c.-88G>A upstream_gene_variant 0.95
pepQ 2859381 c.1038C>G synonymous_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086987 p.Gln56His missense_variant 0.94
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.12
fbiB 3642877 p.Lys448Arg missense_variant 0.93
embC 4242075 p.Arg738Gln missense_variant 0.91
embA 4242643 c.-590C>T upstream_gene_variant 0.98
embC 4242803 p.Val981Leu missense_variant 0.13
ubiA 4269307 p.Phe176Ser missense_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.92