TB-Profiler result

Run: ERR3077965
Summary

Run ID: ERR3077965

Sample name:

Date: 01-04-2023 00:12:52

Number of reads: 486584

Percentage reads mapped: 99.04

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1 East-African-Indian Non-CAS1-Delhi 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288859 p.Val128Gly missense_variant 1.0 pyrazinamide
pncA 2289039 p.Trp68* stop_gained 0.15 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
ethA 4326208 c.1265_1266insT frameshift_variant 1.0 ethionamide
gid 4407731 c.471delG frameshift_variant 1.0 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 6517 p.Leu426Phe missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7953 p.Ala218Ser missense_variant 0.12
gyrA 8018 c.717C>A synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.27
fgd1 491170 c.391delC frameshift_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620115 c.225C>A synonymous_variant 0.12
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760845 p.Thr347Ala missense_variant 0.4
rpoB 761407 p.Val534Ala missense_variant 1.0
rpoB 761733 p.Val643Ile missense_variant 0.17
rpoB 761768 c.1962G>T synonymous_variant 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763772 p.Val135Leu missense_variant 0.17
rpoC 764133 p.Ala255Asp missense_variant 0.11
rpoC 764219 p.Gly284Cys missense_variant 0.2
rpoC 764347 c.978G>T synonymous_variant 0.13
rpoC 766016 p.Asp883Tyr missense_variant 0.12
rpoC 766029 p.Arg887His missense_variant 0.12
rpoC 767135 p.Lys1256Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777554 c.927C>T synonymous_variant 0.13
mmpL5 778042 p.Ala147Ser missense_variant 0.14
rpsL 781392 c.-168C>A upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800640 c.-169A>G upstream_gene_variant 0.12
rplC 801223 p.His139Asn missense_variant 0.2
fbiC 1304895 c.1965C>A synonymous_variant 0.12
Rv1258c 1406825 c.516C>A synonymous_variant 0.12
embR 1416965 p.Ala128Asp missense_variant 0.12
atpE 1461257 p.Met71Ile missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472044 n.199G>T non_coding_transcript_exon_variant 0.12
rrs 1472953 n.1108G>T non_coding_transcript_exon_variant 0.17
rrs 1472997 n.1152G>A non_coding_transcript_exon_variant 0.12
rrl 1473951 n.294G>T non_coding_transcript_exon_variant 0.15
inhA 1674162 c.-40C>A upstream_gene_variant 0.13
inhA 1674553 p.Lys118Glu missense_variant 0.13
inhA 1674853 p.Leu218Ile missense_variant 0.14
tlyA 1917956 p.Arg6Leu missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918258 p.His107Asn missense_variant 0.15
ndh 2102986 c.57C>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155008 c.1104C>T synonymous_variant 0.17
katG 2156079 c.33C>A synonymous_variant 0.13
katG 2156158 c.-47A>G upstream_gene_variant 0.13
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289336 c.-95G>T upstream_gene_variant 0.14
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289869 c.-628G>T upstream_gene_variant 0.12
kasA 2518388 p.Gly92Arg missense_variant 0.12
ahpC 2725995 c.-198A>G upstream_gene_variant 0.11
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746447 c.1152C>T synonymous_variant 0.2
pepQ 2859587 p.Arg278Cys missense_variant 0.11
pepQ 2860516 c.-99dupC upstream_gene_variant 0.14
Rv2752c 3064731 p.Leu487Phe missense_variant 0.14
thyA 3074632 c.-161C>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087473 c.654C>A synonymous_variant 0.12
ald 3087523 p.Val235Ala missense_variant 0.1
fbiD 3339177 c.60C>G synonymous_variant 0.13
Rv3083 3448468 c.-36C>A upstream_gene_variant 0.18
Rv3083 3448632 c.129C>A synonymous_variant 0.17
fprA 3473945 c.-62C>A upstream_gene_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474093 c.87C>A synonymous_variant 0.2
fprA 3475366 p.Gly454Trp missense_variant 0.12
whiB7 3568505 c.175C>A synonymous_variant 0.13
rpoA 3878552 c.-45C>G upstream_gene_variant 0.4
clpC1 4038969 p.Gln579Arg missense_variant 0.12
clpC1 4040053 p.Pro218Ser missense_variant 0.13
embC 4239672 c.-191G>T upstream_gene_variant 0.14
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240835 p.Gly325Cys missense_variant 0.12
embC 4240909 c.1047G>T synonymous_variant 0.14
embC 4240914 p.Met351Thr missense_variant 0.14
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 4243323 p.Val31Ile missense_variant 1.0
embA 4244009 c.777G>T synonymous_variant 0.17
embA 4245113 c.1881C>A synonymous_variant 0.18
embA 4245476 c.2244C>A synonymous_variant 0.12
embA 4245525 p.Gly765Arg missense_variant 0.11
embA 4245691 p.Gly820Val missense_variant 0.15
embA 4245820 p.Ser863Ile missense_variant 0.17
embA 4245879 p.Asp883Tyr missense_variant 0.14
embA 4246336 p.Ala1035Glu missense_variant 0.14
embB 4246783 c.270C>A synonymous_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 0.15
embB 4247790 p.Ser426Ile missense_variant 0.14
embB 4248731 p.Val740Leu missense_variant 0.18
aftB 4267042 p.Arg599Ser missense_variant 0.15
aftB 4267278 p.Arg520Leu missense_variant 0.12
aftB 4269516 c.-680G>T upstream_gene_variant 0.14
ubiA 4269676 p.Ser53Ile missense_variant 0.15
ethA 4326148 c.1326G>A synonymous_variant 0.13
ethA 4327132 p.Asn114Lys missense_variant 0.17
ethR 4328051 p.Ala168Val missense_variant 1.0
ethA 4328335 c.-862C>A upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338615 c.-94C>A upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407737 p.Asn156Tyr missense_variant 0.12