TB-Profiler result

Run: SRR16157104
Summary

Run ID: SRR16157104

Sample name:

Date: 03-04-2023 16:44:21

Number of reads: 917012

Percentage reads mapped: 81.21

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 0.9 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 2288719 p.Met175Val missense_variant 1.0 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 0.95 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 0.1
gyrA 9647 c.2346C>G synonymous_variant 0.23
mshA 576108 p.Ala254Gly missense_variant 0.25
mshA 576453 p.Val369Gly missense_variant 0.25
mshA 576606 p.Ala420Gly missense_variant 0.38
mshA 576609 p.Ala421Gly missense_variant 0.25
mshA 576616 c.1269G>C synonymous_variant 0.4
ccsA 620019 c.129A>C synonymous_variant 0.25
rpoB 763150 p.Phe1115Cys missense_variant 0.16
rpoC 764367 p.Gly333Ala missense_variant 0.37
rpoC 765862 p.Phe831Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777883 p.Gly200Arg missense_variant 0.15
mmpL5 778932 c.-452A>G upstream_gene_variant 0.14
mmpL5 779307 c.-827T>C upstream_gene_variant 0.18
mmpL5 779319 c.-839T>C upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303157 p.His76Pro missense_variant 0.19
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673553 p.Asp38Glu missense_variant 0.29
fabG1 1674065 p.Lys209Thr missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169149 c.1464G>C synonymous_variant 1.0
PPE35 2170035 p.Val193Gly missense_variant 0.33
Rv1979c 2222579 p.Ala196Ser missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288949 p.Ala98Val missense_variant 1.0
kasA 2519071 p.Asp319Glu missense_variant 0.27
folC 2747468 p.Asp44Ile missense_variant 0.91
folC 2747470 p.Ile43Met missense_variant 1.0
thyX 3067944 p.Val1Gly missense_variant 0.3
whiB7 3568485 c.195T>G synonymous_variant 0.29
alr 3840557 c.864T>A synonymous_variant 0.13
alr 3841356 p.Ser22Leu missense_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040550 p.Leu52Trp missense_variant 0.27
embC 4240427 p.Ser189Cys missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243682 c.450T>G synonymous_variant 0.19
embB 4246527 p.Ala5Gly missense_variant 0.3
embB 4247028 p.Leu172Arg missense_variant 0.25
aftB 4267981 p.Arg286Gly missense_variant 0.12
ethA 4326390 p.Asp362His missense_variant 0.2
ethA 4328415 c.-942A>G upstream_gene_variant 0.23
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0
ethA 4326539 c.866_934delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNT disruptive_inframe_deletion 1.0