TB-Profiler result

Run: SRR1181252
Summary

Run ID: SRR1181252

Sample name:

Date: 03-04-2023 04:40:51

Number of reads: 2879915

Percentage reads mapped: 99.12

Strain: lineage4.8;lineage4.1.2;lineage2.2.1

Drug-resistance: Sensitive

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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 0.6
lineage4 Euro-American LAM;T;S;X;H None 0.37
lineage4.1 Euro-American T;X;H None 0.15
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.6
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.18
lineage4.1.2 Euro-American T;H None 0.15
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.63
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
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 0.82
gyrA 9304 p.Gly668Asp missense_variant 0.78
fgd1 491556 c.774G>A synonymous_variant 0.52
fgd1 491742 c.960T>C synonymous_variant 0.59
mshA 575907 p.Ala187Val missense_variant 0.47
ccsA 620625 p.Ile245Met missense_variant 0.69
rpoC 763031 c.-339T>C upstream_gene_variant 0.62
rpoC 765150 p.Gly594Glu missense_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.76
mmpL5 776182 p.Asp767Asn missense_variant 0.81
mmpS5 779615 c.-710C>G upstream_gene_variant 0.48
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 0.41
embR 1417140 p.Ala70Ser missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.16
fabG1 1673249 c.-191C>T upstream_gene_variant 0.15
inhA 1674210 c.9A>C synonymous_variant 0.54
rpsA 1833440 c.-102G>A upstream_gene_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 0.68
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.61
PPE35 2167926 p.Leu896Ser missense_variant 0.61
PPE35 2168524 p.Gly697Ser missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715357 c.-25G>T upstream_gene_variant 0.12
folC 2747022 p.Val193Ile missense_variant 0.22
Rv2752c 3064519 c.1672delG frameshift_variant 0.54
ald 3086788 c.-32T>C upstream_gene_variant 0.7
Rv3083 3448894 p.Tyr131Asp missense_variant 0.31
Rv3083 3449642 p.Asn380Ser missense_variant 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.71
fprA 3475357 p.Leu451Val missense_variant 0.13
Rv3236c 3612813 p.Thr102Ala missense_variant 0.72
fbiA 3641164 p.Ile208Val missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.73
aftB 4267647 p.Asp397Gly missense_variant 0.65
aftB 4268861 c.-25T>C upstream_gene_variant 0.19
whiB6 4338286 p.Val79Ala missense_variant 0.79
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.64
gid 4407927 p.Glu92Asp missense_variant 0.43