TB-Profiler result

Run: ERR028343
Summary

Run ID: ERR028343

Sample name:

Date: 31-03-2023 08:22:59

Number of reads: 699517

Percentage reads mapped: 98.35

Strain: lineage4;lineage3.1.1;lineage1

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 0.29
lineage1 Indo-Oceanic EAI RD239 0.25
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 0.33
lineage3.1.1 East-African-Indian CAS1-Kili RD750 0.11
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 0.25 isoniazid
ethA 4326236 p.Gly413Asp missense_variant 0.12 ethionamide
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 6112 p.Met291Ile missense_variant 0.33
gyrB 6124 c.885C>T synonymous_variant 0.33
gyrB 6446 p.Ala403Ser missense_variant 0.24
gyrB 6934 p.Gln565His missense_variant 0.27
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 0.23
gyrA 9143 c.1842T>C synonymous_variant 0.5
gyrA 9304 p.Gly668Asp missense_variant 0.9
gyrA 9566 c.2265C>T synonymous_variant 0.43
fgd1 491742 c.960T>C synonymous_variant 0.74
mshA 575819 p.Ser158Ala missense_variant 0.18
rpoB 759746 c.-61C>T upstream_gene_variant 0.19
rpoC 762434 c.-936T>G upstream_gene_variant 0.39
rpoC 763031 c.-339T>C upstream_gene_variant 0.71
rpoC 763462 c.93G>A synonymous_variant 0.12
rpoC 763884 p.Ala172Val missense_variant 0.15
rpoC 763886 c.517C>A synonymous_variant 0.16
rpoC 764995 c.1626C>G synonymous_variant 0.25
rpoC 765171 p.Pro601Leu missense_variant 0.33
rpoC 767305 p.Tyr1312* stop_gained 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.46
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800793 c.-16G>C upstream_gene_variant 0.14
fbiC 1302899 c.-32A>G upstream_gene_variant 0.27
Rv1258c 1407180 p.Pro54Leu missense_variant 0.17
Rv1258c 1407273 p.Asp23Val missense_variant 0.29
embR 1417019 p.Cys110Tyr missense_variant 0.33
embR 1417501 c.-154A>C upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473369 n.1524A>G non_coding_transcript_exon_variant 0.29
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.2
inhA 1673338 c.-864G>A upstream_gene_variant 0.25
inhA 1674465 c.264C>T synonymous_variant 0.2
inhA 1674892 p.Asn231Asp missense_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101921 c.1122G>A synonymous_variant 0.19
ndh 2103112 c.-70G>T upstream_gene_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 0.71
PPE35 2167926 p.Leu896Ser missense_variant 0.86
PPE35 2167983 p.Gly877Asp missense_variant 0.17
PPE35 2168149 p.Pro822Ser missense_variant 0.13
PPE35 2168316 p.Thr766Ile missense_variant 0.13
PPE35 2169379 p.Phe412Val missense_variant 0.27
PPE35 2169866 c.747G>C synonymous_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 0.27
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.38
kasA 2518132 c.18C>T synonymous_variant 0.44
kasA 2518144 c.30T>G synonymous_variant 0.15
ahpC 2726051 c.-142G>A upstream_gene_variant 0.42
ahpC 2726105 c.-88G>A upstream_gene_variant 0.31
ahpC 2726261 c.69G>T synonymous_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 0.31
thyA 3073868 p.Thr202Ala missense_variant 0.25
thyA 3074654 c.-183T>G upstream_gene_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 0.53
ald 3087184 c.368_373delCCGACG disruptive_inframe_deletion 0.27
Rv3083 3448714 p.Asp71His missense_variant 0.4
Rv3083 3449644 p.Ala381Thr missense_variant 0.21
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.87
fprA 3474597 c.591C>A synonymous_variant 0.58
fprA 3475017 c.1011G>A synonymous_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 0.2
fprA 3475280 p.Val425Gly missense_variant 0.22
whiB7 3568507 p.Gln58Arg missense_variant 0.23
alr 3840932 c.489C>T synonymous_variant 0.14
ddn 3986987 c.144G>T synonymous_variant 0.33
ddn 3987180 p.Asp113Asn missense_variant 0.27
clpC1 4038287 c.2418C>T synonymous_variant 0.12
clpC1 4040517 p.Val63Ala missense_variant 0.24
panD 4044471 c.-190T>G upstream_gene_variant 0.4
embC 4239843 c.-20A>C upstream_gene_variant 0.31
embC 4239973 c.111T>G synonymous_variant 0.22
embC 4240671 p.Thr270Ile missense_variant 0.67
embC 4241042 p.Asn394Asp missense_variant 0.22
embC 4241429 p.Phe523Val missense_variant 0.38
embC 4241562 p.Arg567His missense_variant 0.27
embC 4242075 p.Arg738Gln missense_variant 0.13
embC 4242476 p.Pro872Ala missense_variant 0.38
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.24
embA 4243848 p.Val206Met missense_variant 0.5
embA 4245147 p.Pro639Ser missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 0.15
embB 4247646 p.Glu378Ala missense_variant 0.5
aftB 4268050 p.Pro263Thr missense_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 0.7
aftB 4269606 c.-770T>C upstream_gene_variant 0.33
ethR 4326928 c.-621G>A upstream_gene_variant 0.3
ethA 4327103 p.Gly124Asp missense_variant 0.2
ethA 4327780 c.-307G>T upstream_gene_variant 0.18
ethA 4328209 c.-736C>A upstream_gene_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.44
gid 4407588 c.615A>G synonymous_variant 0.57
gid 4407873 c.330G>T synonymous_variant 0.16
gid 4407935 p.Leu90Val missense_variant 0.29
gid 4407944 p.Gln87Glu missense_variant 0.32