TB-Profiler result

Run: ERR2514665
Summary

Run ID: ERR2514665

Sample name:

Date: 31-03-2023 20:29:16

Number of reads: 449048

Percentage reads mapped: 99.49

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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
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 6018 p.Phe260Ser missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576064 c.720dupC frameshift_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760566 p.Ser254Thr missense_variant 0.12
rpoB 760618 p.Ile271Asn missense_variant 0.15
rpoB 761304 p.Val500Ile missense_variant 0.11
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765916 c.2547C>T synonymous_variant 1.0
rpoC 766085 p.Pro906Ser missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775647 p.Gln945Arg missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781882 p.Lys108Arg missense_variant 0.14
rplC 801324 p.Asn172Lys missense_variant 0.17
fbiC 1303134 c.204G>T synonymous_variant 0.17
fbiC 1305022 p.His698Tyr missense_variant 0.12
Rv1258c 1406106 p.Asp412Val missense_variant 0.12
Rv1258c 1406205 p.Thr379Met missense_variant 0.14
Rv1258c 1407381 c.-41G>T upstream_gene_variant 0.11
atpE 1460894 c.-151A>G upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674455 p.Gly85Asp missense_variant 0.12
rpsA 1834667 p.Ala376Thr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918247 p.Arg103Leu missense_variant 0.11
ndh 2102141 p.Gly301Asp missense_variant 0.14
ndh 2102162 p.Arg294Gln missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156003 p.Asp37Asn missense_variant 0.11
katG 2156152 c.-41G>A upstream_gene_variant 0.12
katG 2156282 c.-171A>G upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167965 p.Ala883Gly missense_variant 0.13
PPE35 2167967 c.2646A>C synonymous_variant 0.13
PPE35 2167973 c.2640A>G synonymous_variant 0.12
PPE35 2169459 p.Gly385Asp missense_variant 0.13
PPE35 2169974 c.639T>C synonymous_variant 0.17
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222094 c.1071G>T synonymous_variant 0.18
Rv1979c 2223036 c.129A>G synonymous_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289445 c.-206_-205delGG upstream_gene_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2747378 p.Gly74Asp missense_variant 0.14
Rv2752c 3065820 c.372G>T synonymous_variant 0.14
thyX 3067442 c.504C>G synonymous_variant 1.0
thyX 3067527 p.Arg140Leu missense_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474065 p.Ala20Val missense_variant 0.11
fprA 3474498 c.492G>A synonymous_variant 0.15
fbiA 3640421 c.-122C>T upstream_gene_variant 0.17
panD 4044280 c.2T>A start_lost 0.12
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243819 p.Ile196Asn missense_variant 0.11
embA 4245744 p.Pro838Thr missense_variant 0.14
embB 4247252 p.Ser247Pro missense_variant 0.15
embB 4249148 p.Ala879Thr missense_variant 0.17
ethR 4327468 c.-81G>A upstream_gene_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0