TB-Profiler result

Run: ERR1949990
Summary

Run ID: ERR1949990

Sample name:

Date: 31-03-2023 15:36:48

Number of reads: 647265

Percentage reads mapped: 99.09

Strain: lineage4.8

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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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 6675 p.Leu479His missense_variant 0.43
gyrB 6951 p.Leu571Pro missense_variant 0.13
gyrB 7152 p.Leu638Arg missense_variant 0.29
gyrB 7158 p.Asp640Ala missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7444 p.Leu48Arg missense_variant 0.25
gyrA 7971 p.Lys224* stop_gained 0.29
gyrA 8274 p.Lys325* stop_gained 0.36
gyrA 9131 p.Gln610His missense_variant 0.2
gyrA 9813 p.Asn838Tyr missense_variant 0.31
fgd1 491161 p.Glu127* stop_gained 0.23
mshA 576343 c.996C>A synonymous_variant 0.29
mshA 576662 p.Ala439Ser missense_variant 0.22
ccsA 619887 c.-4T>G upstream_gene_variant 0.2
ccsA 620558 p.Gln223Leu missense_variant 0.29
rpoB 761382 p.Thr526Pro missense_variant 0.43
rpoB 762083 c.2277T>C synonymous_variant 0.21
rpoB 763305 p.Ser1167Cys missense_variant 0.29
rpoC 766918 c.3549C>A synonymous_variant 0.27
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775837 p.Thr882Pro missense_variant 0.22
mmpL5 775846 p.Ser879Ala missense_variant 0.27
mmpL5 776128 p.Cys785Ser missense_variant 0.43
mmpL5 776245 p.Ile746Phe missense_variant 0.4
mmpL5 776928 p.Leu518Gln missense_variant 0.21
mmpL5 777246 p.Arg412Gln missense_variant 0.2
mmpS5 778679 p.Ala76Asp missense_variant 0.33
mmpL5 778876 c.-396A>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801104 p.Gln99Leu missense_variant 0.23
rplC 801156 c.348T>G synonymous_variant 0.2
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304027 p.Asn366Thr missense_variant 0.18
embR 1416664 p.Tyr228* stop_gained 0.25
embR 1416862 p.Phe162Leu missense_variant 0.27
embR 1417327 c.21G>C synonymous_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471836 n.-10A>T upstream_gene_variant 0.3
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475050 n.1393A>T non_coding_transcript_exon_variant 0.33
rrl 1475430 n.1773T>A non_coding_transcript_exon_variant 0.33
rrl 1475531 n.1874C>A non_coding_transcript_exon_variant 0.29
rrl 1476164 n.2507A>T non_coding_transcript_exon_variant 0.33
rpsA 1834092 p.Val184Gly missense_variant 0.2
rpsA 1834386 p.Asp282Ala missense_variant 0.22
rpsA 1834413 p.His291Pro missense_variant 0.29
tlyA 1917953 p.Ala5Asp missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918601 p.His221Leu missense_variant 0.38
ndh 2102779 p.Asn88Thr missense_variant 0.22
katG 2154229 p.Val628Gly missense_variant 0.27
katG 2155393 p.Asp240Ala missense_variant 0.43
katG 2155426 p.Tyr229Ser missense_variant 0.38
PPE35 2167669 p.Phe982Ile missense_variant 0.25
PPE35 2167683 p.Leu977Gln missense_variant 0.5
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169063 p.Met517Lys missense_variant 0.29
PPE35 2169917 c.696T>A synonymous_variant 0.29
PPE35 2170048 p.Leu189Val missense_variant 0.33
PPE35 2170053 p.Thr187Ser missense_variant 0.22
Rv1979c 2222230 p.Met312Thr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288694 p.Val183Asp missense_variant 0.22
kasA 2518879 p.Lys255Asn missense_variant 0.22
kasA 2519097 p.Val328Gly missense_variant 0.33
eis 2714812 p.Glu174Ala missense_variant 0.13
ahpC 2726209 p.Ile6Asn missense_variant 0.2
ahpC 2726371 p.Val60Glu missense_variant 0.2
folC 2747457 p.Thr48Pro missense_variant 0.22
folC 2747716 c.-118T>A upstream_gene_variant 0.33
Rv2752c 3065014 p.Val393Ala missense_variant 0.14
Rv2752c 3065901 c.291A>C synonymous_variant 0.22
Rv2752c 3067085 c.-894A>C upstream_gene_variant 0.25
ald 3086929 c.111delA frameshift_variant 0.13
fbiD 3339437 p.Ala107Asp missense_variant 0.22
fbiD 3339698 p.Asp194Ala missense_variant 0.39
fprA 3475161 p.Asn385Lys missense_variant 0.2
fprA 3475331 p.Val442Gly missense_variant 0.22
whiB7 3568454 p.Ile76Leu missense_variant 0.38
whiB7 3568754 c.-75T>A upstream_gene_variant 0.29
Rv3236c 3612128 p.Leu330Arg missense_variant 0.38
Rv3236c 3612895 c.222T>G synonymous_variant 0.38
Rv3236c 3613010 p.Tyr36Phe missense_variant 0.44
fbiA 3640655 p.Asp38Gly missense_variant 0.27
fbiA 3641477 p.Asp312Gly missense_variant 0.2
fbiB 3642216 p.Thr228Pro missense_variant 0.25
fbiB 3642440 c.906A>G synonymous_variant 0.25
fbiB 3642686 p.Leu384Phe missense_variant 0.14
rpoA 3878490 c.18C>G synonymous_variant 0.67
clpC1 4040249 p.Glu152Asp missense_variant 0.18
embC 4241421 p.Glu520Ala missense_variant 0.23
embC 4241705 p.Ser615Ala missense_variant 0.3
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243206 c.-27T>A upstream_gene_variant 0.43
embA 4243912 p.Leu227Arg missense_variant 0.21
embA 4244065 p.Leu278Gln missense_variant 0.17
embA 4245624 p.Ser798Pro missense_variant 0.4
embB 4246127 c.-387A>G upstream_gene_variant 0.14
embB 4246157 c.-357A>G upstream_gene_variant 0.23
embB 4246373 c.-141T>G upstream_gene_variant 0.27
embA 4246402 p.Val1057Gly missense_variant 0.23
embB 4247040 p.Phe176Cys missense_variant 0.27
embB 4248786 p.Asp758Ala missense_variant 0.2
embB 4248806 p.Lys765Gln missense_variant 0.2
embB 4249518 p.His1002Pro missense_variant 0.3
aftB 4266969 p.Pro623Gln missense_variant 0.2
aftB 4267702 p.Trp379Gly missense_variant 0.18
aftB 4267801 c.1036T>C synonymous_variant 0.14
aftB 4267824 p.Val338Gly missense_variant 0.23
aftB 4268086 p.Ser251Ala missense_variant 0.29
aftB 4268821 p.Leu6Val missense_variant 0.27
ethR 4326739 c.-810G>C upstream_gene_variant 0.12
ethR 4328060 p.Leu171Gln missense_variant 0.21
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0