TB-Profiler result

Run: SRR21677854
Summary

Run ID: SRR21677854

Sample name:

Date: 04-04-2023 02:48:26

Number of reads: 310972

Percentage reads mapped: 99.4

Strain: lineage4.1.1.3

Drug-resistance: Other

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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 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 0.98
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
thyA 3074224 p.Trp83* stop_gained 0.17 para-aminosalicylic_acid
ethA 4326426 c.1047delT frameshift_variant 0.14 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 6414 p.Leu392Gln missense_variant 0.11
gyrA 6457 c.-845T>A upstream_gene_variant 0.11
gyrA 7210 c.-92C>T upstream_gene_variant 1.0
gyrA 7275 c.-27C>A upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7424 c.123G>T synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7923 p.His208Asp missense_variant 0.15
gyrA 8937 p.Gly546Ser missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9462 p.Thr721Pro missense_variant 0.17
fgd1 491561 p.His260Arg missense_variant 0.18
rpoB 759744 c.-63G>A upstream_gene_variant 0.18
rpoB 760391 p.Ser195Arg missense_variant 0.43
rpoB 760762 p.Gly319Asp missense_variant 0.17
rpoB 761495 c.1689G>A synonymous_variant 0.12
rpoB 763038 p.Thr1078Ala missense_variant 0.14
rpoC 763708 c.339G>T synonymous_variant 0.11
rpoC 764263 c.894G>T synonymous_variant 0.22
rpoC 764361 p.Asp331Val missense_variant 0.12
rpoC 764425 p.Asn352Lys missense_variant 0.11
rpoC 764808 p.Arg480Leu missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765231 p.Ala621Val missense_variant 0.15
rpoC 765568 p.Met733Ile missense_variant 0.15
rpoC 765856 c.2487T>C synonymous_variant 0.1
rpoC 766212 p.Glu948Gly missense_variant 0.11
rpoC 766417 p.His1016Gln missense_variant 0.11
rpoC 766569 p.Val1067Ala missense_variant 0.13
rpoC 766601 p.Asp1078Tyr missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775976 c.2505G>T synonymous_variant 0.14
mmpL5 776291 c.2190G>C synonymous_variant 0.29
mmpL5 776549 c.1932C>A synonymous_variant 0.13
mmpL5 776994 p.Ser496* stop_gained 0.18
mmpL5 777014 c.1467C>T synonymous_variant 0.18
mmpL5 777417 p.Pro355Leu missense_variant 0.13
mmpL5 777631 p.Arg284Ser missense_variant 0.22
mmpL5 777735 p.Phe249Tyr missense_variant 0.18
mmpL5 778216 p.Ser89Gly missense_variant 0.17
mmpS5 778856 p.Val17Gly missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>C upstream_gene_variant 1.0
rpsL 781482 c.-78A>G upstream_gene_variant 0.11
rplC 800653 c.-156A>G upstream_gene_variant 0.12
rplC 800718 c.-91G>A upstream_gene_variant 0.14
rplC 800856 c.48A>G synonymous_variant 0.2
rplC 800960 p.Gln51Pro missense_variant 0.18
rplC 801007 p.Thr67Ser missense_variant 0.18
Rv1258c 1407076 p.Val89Ile missense_variant 0.15
embR 1416935 p.Leu138Pro missense_variant 0.17
embR 1417113 p.Leu79Met missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473498 n.-160G>A upstream_gene_variant 0.12
rrl 1474773 n.1116C>T non_coding_transcript_exon_variant 0.12
rrl 1476339 n.2682G>A non_coding_transcript_exon_variant 0.11
inhA 1674965 p.Gly255Val missense_variant 0.29
inhA 1674992 p.Ala264Glu missense_variant 0.29
rpsA 1834052 p.Ala171Ser missense_variant 0.11
rpsA 1834407 p.Arg289His missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918110 p.Asp57Glu missense_variant 0.12
tlyA 1918125 p.Trp62Cys missense_variant 0.12
tlyA 1918667 p.Leu243* stop_gained 0.13
ndh 2101695 p.Ala450Ser missense_variant 0.33
ndh 2102665 c.377dupT frameshift_variant 0.14
ndh 2102699 p.Leu115Pro missense_variant 0.14
ndh 2102706 p.Asp113Asn missense_variant 0.12
ndh 2103000 p.His15Asn missense_variant 0.13
ndh 2103181 c.-140delC upstream_gene_variant 0.14
katG 2154703 p.Ser470* stop_gained 0.17
katG 2155505 p.Thr203Ala missense_variant 0.29
katG 2156380 c.-269G>T upstream_gene_variant 0.13
katG 2156421 c.-310G>T upstream_gene_variant 0.13
PPE35 2168498 c.2115G>T synonymous_variant 0.15
PPE35 2168604 p.Pro670Arg missense_variant 0.11
PPE35 2170537 p.Ala26Ser missense_variant 0.2
PPE35 2170780 c.-168G>T upstream_gene_variant 0.12
Rv1979c 2222247 c.918C>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289095 c.147C>T synonymous_variant 0.11
pncA 2289229 p.Ile5Val missense_variant 0.15
pncA 2289289 c.-48G>A upstream_gene_variant 0.15
pncA 2289983 c.-742G>T upstream_gene_variant 0.14
kasA 2518820 p.Gly236Ser missense_variant 0.29
kasA 2519155 c.1041C>A synonymous_variant 0.29
eis 2714808 c.525T>C synonymous_variant 0.12
eis 2714960 p.Ile125Phe missense_variant 0.15
eis 2715173 p.Pro54Thr missense_variant 0.11
eis 2715442 c.-110G>T upstream_gene_variant 0.2
eis 2715476 c.-144C>A upstream_gene_variant 0.2
ahpC 2726322 p.Pro44Thr missense_variant 0.14
ahpC 2726342 c.150G>A synonymous_variant 0.13
ahpC 2726403 p.Leu71Ile missense_variant 0.22
ahpC 2726501 c.312_313delAA frameshift_variant 0.22
ahpC 2726712 p.Cys174Arg missense_variant 0.14
folC 2746579 p.Glu340Asp missense_variant 0.13
folC 2746932 p.Ala223Thr missense_variant 0.22
folC 2747069 p.Met177Thr missense_variant 0.15
pepQ 2859693 c.726C>T synonymous_variant 0.4
pepQ 2860227 c.192C>A synonymous_variant 0.11
pepQ 2860285 p.Val45Ala missense_variant 0.13
pepQ 2860493 c.-75C>A upstream_gene_variant 0.13
ribD 2986669 c.-170G>A upstream_gene_variant 0.12
thyX 3067719 p.Ala76Val missense_variant 0.22
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087060 p.Glu81Lys missense_variant 0.11
Rv3083 3448335 c.-169C>T upstream_gene_variant 0.5
Rv3083 3448869 c.366C>T synonymous_variant 0.13
Rv3083 3449635 p.Leu378Met missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474310 p.Tyr102His missense_variant 0.2
fprA 3475012 p.Asp336Asn missense_variant 0.22
whiB7 3568862 c.-183C>T upstream_gene_variant 0.11
Rv3236c 3612844 c.273G>T synonymous_variant 0.17
fbiA 3640345 c.-198C>T upstream_gene_variant 0.17
fbiA 3640466 c.-77T>A upstream_gene_variant 0.11
fbiB 3640578 c.-957C>T upstream_gene_variant 0.13
fbiB 3641564 c.30G>T synonymous_variant 0.11
fbiB 3641637 p.Ala35Ser missense_variant 0.12
alr 3840452 c.969C>T synonymous_variant 0.5
alr 3840530 p.His297Asn missense_variant 0.17
rpoA 3877676 p.Arg278Cys missense_variant 0.12
clpC1 4038932 c.1773G>T synonymous_variant 0.15
clpC1 4039241 c.1464G>A synonymous_variant 0.33
clpC1 4039844 p.Asp287Glu missense_variant 0.14
embC 4239978 c.117_118delAG frameshift_variant 0.12
embC 4240396 c.534G>A synonymous_variant 0.15
embC 4240548 p.Leu229Pro missense_variant 0.13
embC 4241172 p.Phe437Tyr missense_variant 0.18
embC 4241206 c.1344G>A synonymous_variant 0.18
embC 4241300 p.Ala480Thr missense_variant 0.17
embC 4242593 p.His911Asn missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242701 p.Ala947Ser missense_variant 0.12
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242872 p.Asp1004Asn missense_variant 0.17
embA 4244277 p.Pro349Ala missense_variant 0.33
embA 4244501 c.1269G>T synonymous_variant 0.18
embA 4244860 p.Gly543Glu missense_variant 1.0
embA 4245274 p.Arg681Leu missense_variant 0.17
embA 4245715 p.Leu828Pro missense_variant 0.11
embA 4245738 p.Arg836Ser missense_variant 0.11
embB 4246337 c.-177G>T upstream_gene_variant 0.25
embB 4246578 p.Ser22Tyr missense_variant 0.17
embB 4247284 c.771G>A synonymous_variant 0.2
embB 4247785 c.1272G>T synonymous_variant 0.17
embB 4247956 c.1443G>T synonymous_variant 0.14
embB 4248370 c.1857G>T synonymous_variant 0.11
embB 4248412 p.Phe633Leu missense_variant 0.11
embB 4249021 c.2508G>T synonymous_variant 0.17
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4266982 p.Asp619Tyr missense_variant 0.29
aftB 4267227 p.Val537Leu missense_variant 0.14
aftB 4267405 p.Pro478Thr missense_variant 0.12
aftB 4268089 p.Trp250Arg missense_variant 0.2
aftB 4268449 p.Pro130Thr missense_variant 0.29
aftB 4268562 p.Leu92Pro missense_variant 0.25
aftB 4268678 p.Glu53Asp missense_variant 0.22
ubiA 4269037 p.Val266Ala missense_variant 0.22
ethR 4327854 p.Met102Ile missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338661 c.-140C>A upstream_gene_variant 0.12
gid 4407798 c.405G>T synonymous_variant 1.0