TB-Profiler result

Run: SRR2328057
Summary

Run ID: SRR2328057

Sample name:

Date: 04-04-2023 04:35:10

Number of reads: 1274593

Percentage reads mapped: 97.88

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 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761136 p.Thr444Pro missense_variant 0.31 rifampicin
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 2289096 p.Asp49Ala missense_variant 1.0 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 0.95 para-aminosalicylic_acid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
thyA 3069838 c.-981_*3841del transcript_ablation 1.0 para-aminosalicylic_acid
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 6307 c.-995T>C upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7567 p.Asp89Ala missense_variant 0.33
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7927 p.Asp209Ala missense_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.35
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760407 p.Ser201Arg missense_variant 0.4
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764327 p.Ile320Leu missense_variant 0.41
rpoC 764817 p.Val483Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778288 p.Ser65Arg missense_variant 0.26
mmpL5 778480 c.1A>G start_lost 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304274 p.Asp448Glu missense_variant 0.47
fbiC 1304672 p.Val581Gly missense_variant 0.29
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407039 p.Val101Gly missense_variant 0.33
embR 1416518 p.Leu277Arg missense_variant 0.39
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471946 n.101C>T non_coding_transcript_exon_variant 0.11
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.14
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.18
rrl 1476112 n.2455G>T non_coding_transcript_exon_variant 0.14
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918607 p.Val223Gly missense_variant 0.45
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156552 c.-441C>T upstream_gene_variant 0.95
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169063 p.Met517Lys missense_variant 0.22
PPE35 2169144 p.Val490Glu missense_variant 0.32
PPE35 2169909 p.Asn235Ile missense_variant 0.22
PPE35 2170047 p.Leu189Arg missense_variant 0.44
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067863 p.Asp28Ala missense_variant 0.26
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087183 p.Thr122Pro missense_variant 0.29
fbiD 3339744 c.627A>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474290 p.Glu95Ala missense_variant 0.25
fprA 3474634 p.Leu210Val missense_variant 0.36
whiB7 3568428 c.252A>G synonymous_variant 0.33
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641668 p.Val45Gly missense_variant 0.38
alr 3840225 p.Thr399Ile missense_variant 1.0
clpC1 4039063 p.Ser548Ala missense_variant 0.27
embC 4239868 c.6T>G synonymous_variant 0.19
embC 4240439 p.Phe193Ile missense_variant 0.14
embC 4240495 c.633T>G synonymous_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243192 c.-40delT upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245457 p.Glu742Ala missense_variant 0.32
embA 4245640 p.Asn803Thr missense_variant 0.38
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246584 p.Arg24Pro missense_variant 0.29
embB 4247219 p.Leu236Val missense_variant 0.22
embB 4249725 p.Val1071Gly missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267704 p.Leu378Arg missense_variant 0.35
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338223 p.Glu100Ala missense_variant 0.36
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