TB-Profiler result

Run: ERR4818619
Summary

Run ID: ERR4818619

Sample name:

Date: 01-04-2023 15:39:35

Number of reads: 661378

Percentage reads mapped: 99.45

Strain: lineage3

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
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
gyrA 7099 c.-203G>A upstream_gene_variant 0.11
gyrA 7165 c.-137C>G upstream_gene_variant 0.11
gyrA 7213 c.-89G>A upstream_gene_variant 0.12
gyrA 7216 c.-86G>C upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8383 p.Leu361Pro missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.11
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 759620 c.-187A>C upstream_gene_variant 0.33
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 762485 c.-885G>C upstream_gene_variant 0.2
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763773 p.Val135Ala missense_variant 0.1
rpoC 764662 c.1293G>A synonymous_variant 0.18
rpoC 765852 p.Lys828Arg missense_variant 0.15
rpoC 766307 p.Gly980Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777955 p.Leu176Phe missense_variant 0.12
mmpS5 778758 p.Pro50Ser missense_variant 0.11
mmpL5 779298 c.-818G>A upstream_gene_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302936 c.6G>C synonymous_variant 0.18
Rv1258c 1406354 c.986delA frameshift_variant 0.12
Rv1258c 1406994 p.Phe116Tyr missense_variant 0.14
Rv1258c 1407006 p.Leu112Arg missense_variant 0.2
embR 1416526 c.822C>G synonymous_variant 0.11
embR 1417190 p.Asp53Val missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1833839 p.Leu100Ile missense_variant 0.11
rpsA 1833879 p.Trp113* stop_gained 0.11
tlyA 1917808 c.-132C>G upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917976 p.Arg13Trp missense_variant 0.2
ndh 2101988 p.Ala352Val missense_variant 0.13
ndh 2103225 c.-183A>C upstream_gene_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167745 p.Thr956Arg missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170392 p.Gly74Ala missense_variant 0.15
PPE35 2170400 c.213G>C synonymous_variant 0.15
Rv1979c 2222407 p.Pro253Leu missense_variant 0.12
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 2289888 c.-647G>A upstream_gene_variant 0.15
kasA 2518363 c.249C>T synonymous_variant 0.22
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
ahpC 2726338 p.Val49Gly missense_variant 0.29
folC 2747558 c.40delG frameshift_variant 0.13
ribD 2987296 p.Arg153His missense_variant 0.14
ribD 2987603 c.765C>T synonymous_variant 0.11
Rv2752c 3065218 p.Ser325Asn missense_variant 0.13
Rv2752c 3065264 p.Glu310Gln missense_variant 0.17
thyX 3067235 c.711C>T synonymous_variant 0.18
thyX 3067558 p.His130Tyr missense_variant 0.11
thyA 3073680 c.792A>G stop_lost&splice_region_variant 0.1
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473820 c.-187C>A upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612646 c.471C>T synonymous_variant 0.11
fbiB 3641853 p.Gly107Ser missense_variant 0.22
fbiB 3642339 p.Asp269Asn missense_variant 0.14
rpoA 3877526 p.Gly328Arg missense_variant 0.11
rpoA 3877527 c.981C>A synonymous_variant 0.12
clpC1 4038327 p.Glu793Gly missense_variant 0.13
clpC1 4038650 c.2055C>T synonymous_variant 0.13
clpC1 4038773 p.Asp644Glu missense_variant 0.11
clpC1 4038776 p.Glu643Asp missense_variant 0.1
clpC1 4039484 c.1221T>G synonymous_variant 0.33
embC 4240033 c.171G>A synonymous_variant 0.15
embC 4241387 p.Ser509Arg missense_variant 0.13
embC 4241395 p.Lys511Asn missense_variant 0.15
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242502 c.-731G>A upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245495 p.Gly755Ser missense_variant 0.1
embA 4245772 p.Asn847Thr missense_variant 0.22
embA 4245834 c.2603_2609delTGGTGGT frameshift_variant 0.12
embA 4245844 p.Val871Glu missense_variant 0.12
embA 4245846 p.Ser872Thr missense_variant 0.12
embA 4245848 c.2616_2617insACCACCA frameshift_variant 0.12
embB 4246070 c.-444G>T upstream_gene_variant 0.15
embB 4248317 p.Val602Pro missense_variant 0.11
embB 4248320 p.Gly603Thr missense_variant 0.11
embB 4248476 p.Pro655Ser missense_variant 0.12
embB 4248868 c.2355G>A synonymous_variant 0.11
embB 4249406 p.Pro965Thr missense_variant 0.11
aftB 4267525 p.Val438Met missense_variant 0.25
aftB 4268529 p.Gly103Asp missense_variant 0.2
aftB 4268551 p.Val96Leu missense_variant 0.22
ubiA 4269865 c.-32G>T upstream_gene_variant 0.15
ethA 4326380 p.Thr365Met missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407913 p.Arg97His missense_variant 0.11