TB-Profiler result

Run: ERR7910875
Summary

Run ID: ERR7910875

Sample name:

Date: 02-04-2023 06:33:15

Number of reads: 257294

Percentage reads mapped: 99.46

Strain: lineage4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289213 p.Gln10Pro missense_variant 1.0 pyrazinamide
embB 4247574 p.Asp354Ala missense_variant 0.9 ethambutol
gid 4407773 p.Lys144* stop_gained 0.5 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 6052 p.Ile271Met missense_variant 1.0
gyrA 6703 c.-599G>A upstream_gene_variant 0.5
gyrB 7221 p.Ser661Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7478 p.Met59Ile missense_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 759840 p.Ser12Cys missense_variant 0.5
rpoC 764303 p.Met312Leu missense_variant 0.75
rpoC 764327 p.Ile320Leu missense_variant 0.5
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765513 p.Lys715Thr missense_variant 1.0
rpoC 766311 p.Arg981Leu missense_variant 0.18
rpoC 767058 p.Thr1230Ile missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776443 p.Phe680Val missense_variant 0.38
mmpS5 779579 c.-674T>A upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800855 p.Val16Glu missense_variant 0.29
fbiC 1303199 p.Val90Gly missense_variant 0.29
fbiC 1305040 p.Ser704Ala missense_variant 0.5
fbiC 1305373 p.Thr815Pro missense_variant 0.5
embR 1416699 p.Leu217Val missense_variant 1.0
atpE 1461259 p.Ala72Glu missense_variant 0.29
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473090 n.1245G>T non_coding_transcript_exon_variant 0.2
rrl 1474611 n.954A>T non_coding_transcript_exon_variant 0.4
rrl 1475477 n.1820A>T non_coding_transcript_exon_variant 0.2
rrl 1475839 n.2182T>A non_coding_transcript_exon_variant 0.29
fabG1 1673561 p.Lys41Thr missense_variant 0.4
inhA 1673865 c.-337C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102652 p.Phe131Ile missense_variant 0.33
katG 2155199 p.Gly305Ser missense_variant 0.4
PPE35 2168265 p.Gly783Val missense_variant 0.67
PPE35 2170556 c.57G>T synonymous_variant 0.4
Rv1979c 2221904 p.Ala421Ser missense_variant 0.4
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289507 c.-266A>T upstream_gene_variant 0.29
kasA 2518415 p.Pro101Ala missense_variant 0.33
kasA 2518503 p.Asn130Ile missense_variant 0.25
kasA 2518617 p.Val168Gly missense_variant 0.4
eis 2714832 p.Arg167Ser missense_variant 0.75
thyX 3068031 c.-86A>C upstream_gene_variant 0.4
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3338991 c.-127T>C upstream_gene_variant 0.33
fbiD 3339275 p.Val53Gly missense_variant 0.5
Rv3083 3449746 p.Asp415Asn missense_variant 0.2
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474172 p.Asp56Tyr missense_variant 0.25
whiB7 3568512 c.168G>A synonymous_variant 0.29
Rv3236c 3612096 p.Ile341Phe missense_variant 0.4
fbiB 3641953 p.Leu140Arg missense_variant 0.33
fbiB 3642218 c.684A>C synonymous_variant 0.29
fbiB 3642691 p.Val386Gly missense_variant 0.22
embC 4241058 p.Glu399Val missense_variant 0.5
embC 4241657 p.Ser599Ala missense_variant 0.67
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243420 p.Val63Glu missense_variant 0.33
embA 4243798 p.Val189Gly missense_variant 0.2
embA 4245041 c.1809C>A synonymous_variant 0.22
embA 4245232 p.Arg667Leu missense_variant 0.29
embA 4245402 p.Thr724Pro missense_variant 0.33
embB 4245740 c.-774T>A upstream_gene_variant 0.5
embB 4246934 p.Thr141Ala missense_variant 0.67
embB 4248954 p.Asp814Ala missense_variant 0.18
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4267909 p.Ala310Ser missense_variant 0.4
ubiA 4269716 p.Leu40Val missense_variant 0.43
ethA 4326900 p.Pro192Ser missense_variant 1.0
ethA 4328025 c.-552T>G upstream_gene_variant 0.38
whiB6 4338594 c.-73T>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407718 p.Ile162Ser missense_variant 0.33
gid 4407980 p.Pro75Ser missense_variant 1.0
gid 4408267 c.-65T>G upstream_gene_variant 0.33