TB-Profiler result

Run: SRR11972255
Summary

Run ID: SRR11972255

Sample name:

Date: 03-04-2023 05:33:39

Number of reads: 511644

Percentage reads mapped: 98.84

Strain: lineage3

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 0.88
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.07
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 0.14 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 0.15 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.25 isoniazid
gid 4408100 c.102delG frameshift_variant 0.24 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 7212 p.Ala658Glu missense_variant 0.14
gyrA 7306 p.Thr2Lys 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 491742 c.960T>C synonymous_variant 1.0
fgd1 491790 c.1008C>T synonymous_variant 0.12
mshA 575257 c.-91T>C upstream_gene_variant 0.25
mshA 575417 p.Ala24Thr missense_variant 0.12
mshA 575769 p.Ala141Val missense_variant 0.12
mshA 575907 p.Ala187Val missense_variant 0.12
mshA 576089 p.Arg248Cys missense_variant 0.4
mshA 576485 p.Ala380Ser missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 0.22
rpoB 759746 c.-61C>T upstream_gene_variant 0.92
rpoB 759792 c.-15C>A upstream_gene_variant 0.12
rpoB 759820 p.Arg5His missense_variant 0.13
rpoB 760937 p.Glu377Asp missense_variant 0.12
rpoC 762434 c.-936T>G upstream_gene_variant 0.88
rpoC 762716 c.-654G>C upstream_gene_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765840 p.Val824Ala missense_variant 0.13
rpoC 766429 c.3060C>T synonymous_variant 0.12
rpoC 767172 p.Arg1268Leu missense_variant 0.17
rpoC 767204 p.Arg1279Cys missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.21
mmpL5 776583 p.Gln633Arg missense_variant 0.11
mmpL5 777264 p.Leu406Pro missense_variant 0.18
mmpL5 777290 c.1191G>A synonymous_variant 0.2
mmpL5 777395 c.1086C>T synonymous_variant 0.18
mmpL5 777420 p.Gly354Asp missense_variant 0.22
mmpR5 779245 p.Ala86Thr missense_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304194 p.Thr422Ala missense_variant 0.22
fbiC 1305494 c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT frameshift_variant&stop_lost&splice_region_variant 0.33
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14
atpE 1460876 c.-169G>A upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 0.98
fabG1 1673672 p.His78Leu missense_variant 0.12
fabG1 1673929 p.Ala164Ser missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.19
rpsA 1834487 p.Gly316Ser missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918190 p.Arg84Gln missense_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155623 c.489C>T synonymous_variant 0.17
katG 2156048 p.Val22Phe missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.18
PPE35 2169910 p.Asn235Tyr missense_variant 0.16
PPE35 2169939 p.Gly225Ala missense_variant 0.11
PPE35 2169944 c.669G>C synonymous_variant 0.11
PPE35 2169947 c.666T>C synonymous_variant 0.11
PPE35 2170052 c.561C>T synonymous_variant 0.14
PPE35 2170308 p.Leu102Ala missense_variant 0.11
Rv1979c 2222344 p.Ala274Val missense_variant 0.85
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 0.94
pncA 2289365 c.-125delC upstream_gene_variant 0.83
pncA 2289433 c.-192C>T upstream_gene_variant 0.12
kasA 2518429 c.315A>C synonymous_variant 0.15
eis 2714641 p.Thr231Ile missense_variant 0.12
eis 2714846 p.Val163Ile missense_variant 0.12
ahpC 2726105 c.-88G>A upstream_gene_variant 0.97
pepQ 2859357 c.1062C>T synonymous_variant 0.12
pepQ 2859631 p.Ala263Glu missense_variant 0.15
pepQ 2860298 p.Gly41Ser missense_variant 0.18
ribD 2986708 c.-131G>A upstream_gene_variant 0.15
ribD 2986993 p.Gly52Asp missense_variant 0.13
thyX 3067864 p.Asp28Tyr missense_variant 0.33
thyA 3073978 p.Gln165Pro missense_variant 0.17
thyA 3074226 c.246A>G synonymous_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087500 c.681T>C synonymous_variant 0.11
ald 3087584 c.765C>A synonymous_variant 0.12
fbiD 3339409 p.Ala98Thr missense_variant 0.12
Rv3083 3449751 c.1248C>T synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641028 p.Glu162Asp missense_variant 0.12
fbiB 3642180 p.Val216Met missense_variant 0.12
fbiB 3642297 p.Gln255* stop_gained 0.17
fbiB 3642745 p.Ala404Val missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.17
ddn 3986705 c.-139C>T upstream_gene_variant 0.89
clpC1 4039061 c.1644G>A synonymous_variant 0.12
clpC1 4040139 p.Pro189Gln missense_variant 0.15
clpC1 4040857 c.-153C>T upstream_gene_variant 0.12
embC 4240410 p.Pro183Leu missense_variant 0.12
embC 4241132 p.Pro424Ser missense_variant 0.18
embC 4241931 p.Thr690Ile missense_variant 0.18
embC 4242075 p.Arg738Gln missense_variant 0.68
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.26
embA 4244342 c.1110C>T synonymous_variant 0.13
embB 4246694 p.Arg61Trp missense_variant 0.14
embB 4247452 c.939C>A synonymous_variant 0.12
aftB 4267293 p.Ala515Val missense_variant 0.22
aftB 4267434 p.Pro468Leu missense_variant 0.13
ubiA 4269193 p.Thr214Ile missense_variant 0.13
ethA 4327629 c.-156C>A upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4408062 c.141G>A synonymous_variant 0.12