TB-Profiler result

Run: SRR3105752
Summary

Run ID: SRR3105752

Sample name:

Date: 04-04-2023 05:08:23

Number of reads: 6128604

Percentage reads mapped: 98.82

Strain: lineage4.1.2;lineage1.2.2.2

Drug-resistance: MDR-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 0.27
lineage1 Indo-Oceanic EAI RD239 0.7
lineage4.1 Euro-American T;X;H None 0.25
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.74
lineage4.1.2 Euro-American T;H None 0.27
lineage1.2.2.2 Indo-Oceanic NA RD239 0.72
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
rpoB 761095 p.Leu430Pro missense_variant 0.14 rifampicin
rpoB 761110 p.Asp435Gly missense_variant 0.18 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.81 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.29 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Pro missense_variant 0.3 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 0.8 kanamycin
embB 4247431 p.Met306Ile missense_variant 0.28 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.78 ethambutol
gid 4407851 c.351dupG frameshift_variant 0.69 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
gyrB 5075 c.-165C>T upstream_gene_variant 0.71
gyrB 6112 p.Met291Ile missense_variant 0.7
gyrA 7268 c.-34C>T upstream_gene_variant 0.79
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.72
gyrA 9143 c.1842T>C synonymous_variant 0.73
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.18
fgd1 491742 c.960T>C synonymous_variant 0.77
rpoB 760115 c.309C>T synonymous_variant 0.28
rpoB 761850 p.Pro682Ala missense_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 0.65
rpoC 763884 p.Ala172Val missense_variant 0.8
rpoC 763886 c.517C>A synonymous_variant 0.81
rpoC 764263 c.894G>A synonymous_variant 0.25
rpoC 765148 c.1779C>T synonymous_variant 0.82
rpoC 765150 p.Gly594Glu missense_variant 0.17
rpoC 767314 p.Tyr1315* stop_gained 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775895 c.2586C>T synonymous_variant 0.28
mmpL5 776100 p.Thr794Ile missense_variant 0.69
mmpL5 777320 c.1161C>G synonymous_variant 0.21
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 0.71
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.76
PPE35 2167926 p.Leu896Ser missense_variant 0.7
PPE35 2168742 p.Gly624Asp missense_variant 0.83
Rv1979c 2222308 p.Asp286Gly missense_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.28
kasA 2518132 c.18C>T synonymous_variant 0.73
ahpC 2726051 c.-142G>A upstream_gene_variant 0.78
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.78
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.75
fprA 3475159 p.Asn385Asp missense_variant 0.76
Rv3236c 3611974 c.1143A>C synonymous_variant 0.21
ddn 3987259 p.Trp139* stop_gained 0.23
clpC1 4040517 p.Val63Ala missense_variant 0.71
embC 4240671 p.Thr270Ile missense_variant 0.71
embC 4240975 c.1113C>T synonymous_variant 0.73
embC 4241042 p.Asn394Asp missense_variant 0.6
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.24
embB 4245710 c.-804G>A upstream_gene_variant 0.74
embA 4245969 p.Pro913Ser missense_variant 0.72
embB 4247646 p.Glu378Ala missense_variant 0.69
embB 4247828 p.Ala439Thr missense_variant 0.67
ubiA 4269307 p.Phe176Ser missense_variant 0.3
ubiA 4269387 p.Glu149Asp missense_variant 0.71
aftB 4269606 c.-770T>C upstream_gene_variant 0.66
ethA 4326148 c.1326G>T synonymous_variant 0.72
ethA 4326197 p.Val426Gly missense_variant 0.27
ethA 4326439 p.Asn345Lys missense_variant 0.82
whiB6 4338203 p.Arg107Cys missense_variant 0.72
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.8
gid 4407588 c.615A>G synonymous_variant 0.67
gid 4407873 c.330G>T synonymous_variant 0.7