TB-Profiler result

Run: SRR6797541

Summary

Run ID: SRR6797541

Sample name:

Date: 04-04-2023 16:12:05

Number of reads: 2484835

Percentage reads mapped: 99.37

Strain: lineage4.1.1.1;lineage1.2.2.2

Drug-resistance: HR-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 0.23
lineage1 Indo-Oceanic EAI RD239 0.74
lineage4.1 Euro-American T;X;H None 0.18
lineage1.2.2 Indo-Oceanic EAI1 RD239 0.77
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.22
lineage1.2.2.2 Indo-Oceanic NA RD239 0.78
lineage4.1.1.1 Euro-American (X-type) X2 RD183 0.21
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
katG 2155168 p.Ser315Thr missense_variant 0.14 isoniazid
gid 4408115 c.87delC frameshift_variant 0.15 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 0.8
gyrB 6112 p.Met291Ile missense_variant 0.79
gyrA 7268 c.-34C>T upstream_gene_variant 0.77
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.88
gyrA 9143 c.1842T>C synonymous_variant 0.85
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.78
fgd1 491781 c.999G>A synonymous_variant 0.24
rpoB 761428 p.Pro541Leu missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 0.78
rpoC 763884 p.Ala172Val missense_variant 0.69
rpoC 763886 c.517C>A synonymous_variant 0.7
rpoC 765150 p.Gly594Glu missense_variant 0.31
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.84
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
tlyA 1918004 p.Gln22Arg missense_variant 0.85
tlyA 1918162 p.Glu75Lys missense_variant 0.79
katG 2154724 p.Arg463Leu missense_variant 0.88
PPE35 2167926 p.Leu896Ser missense_variant 0.87
PPE35 2168742 p.Gly624Asp missense_variant 0.81
Rv1979c 2222308 p.Asp286Gly missense_variant 0.74
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.87
ahpC 2725989 c.-204A>G upstream_gene_variant 0.11
ahpC 2726051 c.-142G>A upstream_gene_variant 0.72
folC 2746590 p.Gly337Cys missense_variant 0.18
pepQ 2860186 p.Ala78Val missense_variant 0.79
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.77
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.76
fprA 3475159 p.Asn385Asp missense_variant 0.78
Rv3236c 3612984 p.Asn45His missense_variant 0.69
fbiA 3641447 p.Thr302Met missense_variant 0.19
alr 3840864 p.Asp186Gly missense_variant 0.24
rpoA 3877553 p.Glu319Lys missense_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 0.81
panD 4044305 c.-24C>T upstream_gene_variant 0.9
embC 4240390 p.Asn176Lys missense_variant 0.25
embC 4240671 p.Thr270Ile missense_variant 0.61
embC 4240897 c.1035C>G synonymous_variant 0.17
embC 4241042 p.Asn394Asp missense_variant 0.78
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.23
embA 4245969 p.Pro913Ser missense_variant 0.71
embB 4247646 p.Glu378Ala missense_variant 0.74
embB 4249408 c.2895G>A synonymous_variant 0.25
ubiA 4269387 p.Glu149Asp missense_variant 0.84
aftB 4269606 c.-770T>C upstream_gene_variant 0.74
ethA 4326148 c.1326G>T synonymous_variant 0.71
ethA 4326439 p.Asn345Lys missense_variant 0.83
ethA 4327161 p.Ile105Leu missense_variant 0.18
ethA 4327297 p.Met59Ile missense_variant 0.85
ethR 4327694 p.Asp49Ala missense_variant 0.77
whiB6 4338203 p.Arg107Cys missense_variant 0.74
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.81
gid 4407551 p.Met218Val missense_variant 0.15
gid 4407588 c.615A>G synonymous_variant 0.84
gid 4407611 p.Pro198Ala missense_variant 0.14
gid 4407873 c.330G>T synonymous_variant 0.87