TB-Profiler result

Run: SRR4035772
Summary

Run ID: SRR4035772

Sample name:

Date: 04-04-2023 07:17:22

Number of reads: 1150088

Percentage reads mapped: 99.44

Strain: lineage4.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H 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
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 5983 c.744C>T synonymous_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9404 p.Gln701His missense_variant 0.12
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575306 c.-42T>C upstream_gene_variant 0.11
mshA 575318 c.-30T>C upstream_gene_variant 0.11
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761181 p.Arg459Gly missense_variant 0.11
rpoB 762933 p.Tyr1043Asn missense_variant 0.14
rpoC 763336 c.-34A>G upstream_gene_variant 0.18
rpoC 763453 p.Lys29Gln missense_variant 0.13
rpoC 763973 p.Glu202Lys missense_variant 0.15
rpoC 763979 p.Glu204Lys missense_variant 0.15
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 764814 p.Gln482Pro missense_variant 0.12
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766025 p.Val886Met missense_variant 0.14
rpoC 766861 c.3492G>C synonymous_variant 0.1
rpoC 767034 p.Ser1222* stop_gained 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775758 p.Thr908Ile missense_variant 0.18
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpL5 777826 c.655T>C synonymous_variant 0.11
mmpL5 777834 p.Ile216Thr missense_variant 0.11
mmpS5 778845 p.Ala21Pro missense_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781894 p.Gln112Arg missense_variant 0.12
rpsL 781904 c.345C>T synonymous_variant 0.13
fbiC 1305052 p.Met708Leu missense_variant 0.15
Rv1258c 1406341 p.Tyr334His missense_variant 0.12
Rv1258c 1406409 p.Leu311Gln missense_variant 0.14
embR 1416582 p.Arg256Cys missense_variant 0.13
embR 1416981 p.Val123Leu missense_variant 0.12
embR 1417334 c.13delG frameshift_variant 0.18
rrs 1471657 n.-189G>C upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471690 n.-156G>C upstream_gene_variant 0.17
rrs 1472550 n.707delA non_coding_transcript_exon_variant 0.15
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.25
rrl 1475339 n.1682T>C non_coding_transcript_exon_variant 0.4
rrl 1475499 n.1842C>T non_coding_transcript_exon_variant 0.14
rrl 1475533 n.1876A>T non_coding_transcript_exon_variant 0.22
rrl 1475870 n.2213G>C non_coding_transcript_exon_variant 0.13
rrl 1476589 n.2932G>C non_coding_transcript_exon_variant 0.12
rrl 1476600 n.2947delG non_coding_transcript_exon_variant 0.13
rrl 1476739 n.3082T>C non_coding_transcript_exon_variant 0.12
fabG1 1674038 p.Gln200Arg missense_variant 0.15
fabG1 1674173 p.Met245Thr missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101979 p.Asn355Ile missense_variant 0.12
ndh 2103031 p.Gln4His missense_variant 0.12
katG 2154384 p.Gln576His missense_variant 0.12
katG 2154649 p.Lys488Arg missense_variant 0.15
katG 2154662 p.Arg484Cys missense_variant 0.2
katG 2154673 p.Ala480Gly missense_variant 0.2
katG 2154676 p.Ala479Val missense_variant 0.18
katG 2154839 p.Arg425Gly missense_variant 0.12
katG 2154847 p.Pro422Leu missense_variant 0.14
PPE35 2167657 p.Thr986Pro missense_variant 0.15
PPE35 2168267 c.2346T>C synonymous_variant 0.12
PPE35 2168659 p.Thr652Pro missense_variant 0.11
PPE35 2168735 p.Ser626Arg missense_variant 0.13
PPE35 2168939 p.Leu558Phe missense_variant 0.12
PPE35 2169451 p.Asn388Tyr missense_variant 0.14
PPE35 2170407 p.Ala69Val missense_variant 0.17
Rv1979c 2222661 c.504A>G synonymous_variant 0.11
Rv1979c 2222912 p.Ala85Thr missense_variant 0.17
Rv1979c 2223222 c.-58T>A upstream_gene_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288940 p.Gly101Ala missense_variant 0.12
pncA 2288947 p.Tyr99Asn missense_variant 0.13
pncA 2290204 c.-963G>A upstream_gene_variant 0.14
kasA 2517937 c.-178G>C upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518388 p.Gly92Arg missense_variant 0.12
kasA 2519099 p.Ala329Pro missense_variant 0.14
eis 2714249 p.Gly362* stop_gained 0.14
eis 2714797 p.Tyr179Cys missense_variant 0.11
eis 2715076 p.Ala86Gly missense_variant 0.13
eis 2715081 c.252C>T synonymous_variant 0.13
ahpC 2725965 c.-228T>C upstream_gene_variant 0.15
ahpC 2726514 p.Phe108Ile missense_variant 0.14
ahpC 2726605 p.Val138Asp missense_variant 0.14
folC 2746538 p.His354Leu missense_variant 0.15
folC 2746913 p.Asp229Gly missense_variant 0.12
Rv2752c 3065074 c.1117delT frameshift_variant 0.12
Rv2752c 3065524 p.His223Arg missense_variant 0.11
Rv2752c 3066257 c.-66G>A upstream_gene_variant 0.14
Rv2752c 3066282 c.-91G>T upstream_gene_variant 0.17
Rv2752c 3066292 c.-101A>C upstream_gene_variant 0.17
Rv2752c 3066300 c.-109G>A upstream_gene_variant 0.18
thyX 3067291 p.Leu219Phe missense_variant 0.15
thyX 3068105 c.-160C>T upstream_gene_variant 0.12
thyX 3068114 c.-169G>T upstream_gene_variant 0.13
thyA 3073686 c.785delC frameshift_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086793 c.-27A>G upstream_gene_variant 0.12
ald 3086935 p.Ala39Asp missense_variant 0.13
ald 3087834 c.1015C>T synonymous_variant 0.14
fbiD 3339460 p.Gly115Arg missense_variant 0.15
Rv3083 3448316 c.-188C>A upstream_gene_variant 0.17
Rv3083 3448341 c.-163A>G upstream_gene_variant 0.12
Rv3083 3448677 p.Asp58Glu missense_variant 0.14
Rv3083 3449031 c.528C>G synonymous_variant 0.15
fprA 3473870 c.-137C>T upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568815 c.-137delC upstream_gene_variant 0.15
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3613047 p.Val24Leu missense_variant 0.18
fbiA 3641269 p.Tyr243His missense_variant 0.1
fbiB 3641791 p.Leu86Ser missense_variant 0.18
alr 3840644 c.777G>A synonymous_variant 0.25
alr 3840842 c.579G>A synonymous_variant 0.21
alr 3841025 c.396G>C synonymous_variant 0.13
alr 3841350 p.Ala24Gly missense_variant 0.12
rpoA 3878325 c.183C>T synonymous_variant 0.17
ddn 3987274 p.Ile144Asn missense_variant 0.12
clpC1 4038243 p.Thr821Ser missense_variant 0.11
panD 4043905 p.Glu126Gly missense_variant 0.11
embC 4240664 p.Trp268Arg missense_variant 0.13
embC 4242188 c.2329delC frameshift_variant 0.17
embC 4242311 p.Gly817Arg missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243147 c.-86G>A upstream_gene_variant 0.12
embA 4243830 p.Gly200Cys missense_variant 0.18
embA 4244092 p.Ala287Val missense_variant 0.12
embA 4245775 c.2545delG frameshift_variant 0.12
embB 4247306 p.Met265Leu missense_variant 0.12
embB 4248001 p.Asp496Glu missense_variant 0.12
embB 4248080 c.1567C>T synonymous_variant 0.12
embB 4248987 p.Gly825Asp missense_variant 0.13
embB 4248994 c.2481T>C synonymous_variant 0.12
embB 4249031 p.Ala840Pro missense_variant 0.11
embB 4249046 p.Ala845Thr missense_variant 0.18
embB 4249079 p.Ser856Cys missense_variant 0.17
embB 4249718 p.Thr1069Ala missense_variant 0.2
aftB 4267371 p.Thr489Ile missense_variant 0.14
aftB 4267416 p.Pro474Arg missense_variant 0.12
aftB 4267420 p.Ala473Thr missense_variant 0.14
aftB 4267557 p.Ala427Gly missense_variant 0.12
aftB 4267716 p.Ala374Val missense_variant 0.18
ethR 4327114 c.-435G>A upstream_gene_variant 0.12
ethA 4328273 c.-800C>A upstream_gene_variant 0.17
ethA 4328383 c.-910A>G upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0