TB-Profiler result

Run: SRR6257010
Summary

Run ID: SRR6257010

Sample name:

Date: 04-04-2023 13:22:49

Number of reads: 783015

Percentage reads mapped: 100.0

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4248002 p.Gln497Lys missense_variant 1.0 ethambutol
ethA 4327363 c.110delA frameshift_variant 1.0 ethionamide, 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 6524 p.Arg429Cys missense_variant 1.0
gyrA 6922 c.-380G>T upstream_gene_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7605 p.Pro102Ser missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491586 p.Met268Ile missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575619 p.Arg91Leu missense_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 619827 c.-64C>A upstream_gene_variant 0.12
ccsA 619959 c.69G>C synonymous_variant 0.15
ccsA 620508 c.618A>C synonymous_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620687 p.Thr266Met missense_variant 0.4
rpoB 761342 p.Lys512Asn missense_variant 0.11
rpoB 761490 p.Val562Met missense_variant 0.15
rpoC 762737 c.-633C>G upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763921 c.552G>C synonymous_variant 0.12
rpoC 764260 p.Lys297Asn missense_variant 0.2
rpoC 764587 c.1218C>T synonymous_variant 0.15
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765173 p.Ala602Ser missense_variant 0.17
rpoC 766389 p.Gly1007Asp missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776225 p.Glu752Asp missense_variant 0.13
mmpL5 776988 p.Pro498Leu missense_variant 0.12
mmpL5 777750 p.Arg244His missense_variant 0.13
mmpL5 777807 p.Ser225Leu missense_variant 0.13
mmpS5 778595 p.Leu104Pro missense_variant 0.11
mmpS5 778899 p.Gly3Arg missense_variant 0.12
mmpL5 778916 c.-436G>C upstream_gene_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303114 p.Ala62Thr missense_variant 0.17
fbiC 1303642 p.Pro238Ser missense_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416520 c.828G>A synonymous_variant 0.18
atpE 1461079 p.Gly12Asp missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475611 n.1954T>C non_coding_transcript_exon_variant 0.12
rrl 1476564 n.2907G>A non_coding_transcript_exon_variant 0.12
rrl 1476778 n.3121G>A non_coding_transcript_exon_variant 0.14
inhA 1674456 c.255C>T synonymous_variant 0.13
rpsA 1833343 c.-199G>A upstream_gene_variant 0.25
rpsA 1833386 c.-156A>G upstream_gene_variant 0.25
rpsA 1833977 p.Gly146Ser missense_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918135 p.Gly66Arg missense_variant 0.15
tlyA 1918303 c.364C>T synonymous_variant 0.15
ndh 2102446 c.597C>G synonymous_variant 0.17
ndh 2102564 p.Arg160Pro missense_variant 0.13
katG 2154043 p.Thr690Ile missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154803 c.1309C>T synonymous_variant 0.15
katG 2156428 c.-317C>T upstream_gene_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168208 p.Asp802Val missense_variant 0.15
PPE35 2169087 p.Pro509Leu missense_variant 0.14
PPE35 2169684 p.Gly310Asp missense_variant 0.11
PPE35 2169912 p.Asn234Ser missense_variant 0.13
PPE35 2170166 c.447G>C synonymous_variant 0.14
PPE35 2170212 p.Ala134Glu missense_variant 0.12
PPE35 2170371 p.Thr81Ile missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223364 c.-200G>T upstream_gene_variant 0.11
pncA 2289240 c.2T>C start_lost 1.0
pncA 2289650 c.-409G>C upstream_gene_variant 0.11
pncA 2289874 c.-633C>G upstream_gene_variant 0.1
kasA 2518475 c.361A>C synonymous_variant 0.12
kasA 2519215 c.1101C>T synonymous_variant 0.13
eis 2714410 p.Arg308Pro missense_variant 0.12
eis 2715499 c.-167C>T upstream_gene_variant 0.17
folC 2747580 p.Gly7Ser missense_variant 0.12
pepQ 2859529 p.Gly297Asp missense_variant 0.15
pepQ 2859737 p.Gly228Arg missense_variant 0.17
ribD 2987220 p.Arg128Cys missense_variant 0.12
ribD 2987487 p.Pro217Thr missense_variant 0.25
thyX 3067874 c.72C>A synonymous_variant 0.15
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339486 p.Gln123His missense_variant 0.11
fbiD 3339528 c.411C>T synonymous_variant 0.12
Rv3083 3448840 p.Gln113* stop_gained 0.14
Rv3083 3449067 c.564G>A synonymous_variant 0.25
Rv3083 3449093 c.592_600delGGCTCCAAC conservative_inframe_deletion 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474119 p.Met38Thr missense_variant 0.11
fprA 3474881 p.Asn292Ile missense_variant 0.17
fprA 3475071 p.Tyr355* stop_gained 0.12
whiB7 3568460 p.Gly74Cys missense_variant 0.12
Rv3236c 3612579 p.Glu180Lys missense_variant 0.15
Rv3236c 3612589 c.528C>A synonymous_variant 0.14
Rv3236c 3612670 c.447G>A synonymous_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641345 p.Thr268Ile missense_variant 0.17
fbiB 3642242 c.708C>T synonymous_variant 0.12
clpC1 4040297 p.Gln136His missense_variant 0.18
panD 4044089 p.Gly65Ser missense_variant 0.17
panD 4044127 p.Gly52Val missense_variant 0.14
panD 4044348 c.-67G>A upstream_gene_variant 0.14
embC 4240684 c.822C>T synonymous_variant 0.15
embA 4242373 c.-860C>T upstream_gene_variant 0.14
embC 4242556 p.Leu898Phe missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242736 c.-497C>A upstream_gene_variant 0.2
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243710 p.Gly160Arg missense_variant 0.15
embA 4243924 p.Arg231His missense_variant 0.14
embA 4244473 p.Val414Glu missense_variant 0.15
embA 4245561 p.Val777Met missense_variant 0.17
embA 4245690 p.Gly820Arg missense_variant 0.14
embB 4246892 p.Asp127Asn missense_variant 0.12
embB 4247231 p.Asp240Asn missense_variant 0.11
embB 4248621 p.Thr703Met missense_variant 0.17
aftB 4267482 p.Leu452Ser missense_variant 0.11
aftB 4267615 p.Val408Ile missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269238 p.Ala199Val missense_variant 0.11
ubiA 4269401 p.Gln145Lys missense_variant 0.12
ethA 4326016 c.1458G>A synonymous_variant 0.12
ethA 4326514 c.960C>T synonymous_variant 0.2
ethR 4327847 p.Glu100Gly missense_variant 0.12
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407845 p.Glu120Lys missense_variant 0.15
gid 4407927 p.Glu92Asp missense_variant 1.0