TB-Profiler result

Run: ERR2229584

Summary

Run ID: ERR2229584

Sample name:

Date: 31-03-2023 17:20:22

Number of reads: 768803

Percentage reads mapped: 98.98

Strain: lineage4.8

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
lineage4.8 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
pncA 2289036 p.Pro69Arg missense_variant 0.18 pyrazinamide
pncA 2289171 p.Gly24Asp missense_variant 0.17 pyrazinamide
embB 4247403 p.Ser297Leu missense_variant 0.14 ethambutol
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7646 c.345C>T synonymous_variant 0.14
gyrA 9140 p.Gln613His missense_variant 0.12
gyrA 9222 p.Asp641Asn missense_variant 0.12
fgd1 490898 p.Asp39Ala missense_variant 0.2
mshA 575378 p.Gly11Arg missense_variant 0.12
mshA 575418 p.Ala24Gly missense_variant 0.12
mshA 575422 c.77_78delGC frameshift_variant 0.15
mshA 575651 p.Arg102Gly missense_variant 0.18
mshA 576108 p.Ala254Gly missense_variant 0.18
ccsA 619712 c.-179G>T upstream_gene_variant 0.15
ccsA 620375 c.487delG frameshift_variant 0.22
rpoB 760305 p.Arg167Ser missense_variant 0.14
rpoC 762582 c.-788T>C upstream_gene_variant 0.2
rpoC 764023 c.654G>T synonymous_variant 0.12
rpoC 764531 p.Gly388Cys missense_variant 0.29
rpoC 764541 p.Val391Gly missense_variant 0.5
rpoC 764543 p.Thr392Asp missense_variant 0.5
rpoC 765003 c.1635delG frameshift_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777838 p.Ile215Val missense_variant 0.12
mmpR5 778295 c.-695C>T upstream_gene_variant 0.13
mmpR5 778999 p.Asn4Asp missense_variant 0.12
mmpL5 779467 c.-987G>T upstream_gene_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801120 c.312G>A synonymous_variant 0.4
fbiC 1302768 c.-163G>T upstream_gene_variant 0.14
fbiC 1303442 p.Leu171Ser missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303908 c.978C>G synonymous_variant 0.25
fbiC 1304537 p.Arg536His missense_variant 0.2
embR 1416879 p.Gln157Lys missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474219 n.562G>C non_coding_transcript_exon_variant 0.2
rrl 1474603 n.946C>A non_coding_transcript_exon_variant 0.12
rrl 1474774 n.1117A>G non_coding_transcript_exon_variant 0.13
rrl 1475184 n.1527T>C non_coding_transcript_exon_variant 0.17
rrl 1475280 n.1623G>T non_coding_transcript_exon_variant 0.25
rrl 1475818 n.2161T>C non_coding_transcript_exon_variant 0.11
rpsA 1834922 p.Gly461Cys missense_variant 0.22
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155646 p.Gly156Ser missense_variant 0.13
katG 2155797 p.Met105Ile missense_variant 0.14
katG 2155814 p.Pro100Ser missense_variant 0.15
PPE35 2167868 c.2745A>C synonymous_variant 0.14
PPE35 2168047 p.Leu856Val missense_variant 0.14
PPE35 2168051 c.2562G>C synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169278 c.1335T>C synonymous_variant 0.19
PPE35 2169281 c.1332T>G synonymous_variant 0.18
PPE35 2169457 p.His386Asp missense_variant 0.19
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2170048 p.Leu189Val missense_variant 0.51
PPE35 2170053 p.Thr187Ser missense_variant 0.52
PPE35 2170159 p.Ala152Ser missense_variant 0.14
PPE35 2170238 c.375T>G synonymous_variant 0.25
PPE35 2170528 p.Ser29Ala missense_variant 0.14
PPE35 2170535 c.78G>C synonymous_variant 0.14
Rv1979c 2222286 c.879G>A synonymous_variant 0.13
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289289 c.-48G>C upstream_gene_variant 0.17
kasA 2518727 c.613C>T synonymous_variant 0.2
kasA 2518879 c.765A>G synonymous_variant 0.22
kasA 2518882 c.768C>A synonymous_variant 0.22
kasA 2519272 c.1158C>T synonymous_variant 0.15
eis 2714761 p.Leu191Gln missense_variant 0.22
eis 2714985 c.348G>T synonymous_variant 0.17
eis 2715571 c.-239G>A upstream_gene_variant 0.25
pepQ 2859522 c.897C>A synonymous_variant 0.2
ribD 2987383 p.Leu182His missense_variant 0.14
Rv2752c 3066261 c.-70G>T upstream_gene_variant 0.19
thyX 3067311 c.634delG frameshift_variant 0.18
thyA 3073904 p.Ala190Thr missense_variant 0.13
ald 3087214 p.Pro132Leu missense_variant 0.17
Rv3083 3448333 c.-171G>T upstream_gene_variant 0.18
whiB7 3568592 p.Ala30Thr missense_variant 0.13
whiB7 3568649 p.Pro11Thr missense_variant 0.18
Rv3236c 3612259 c.858G>A synonymous_variant 0.2
Rv3236c 3612666 p.Val151Leu missense_variant 0.17
Rv3236c 3613105 c.12G>A synonymous_variant 0.29
fbiA 3640954 p.Pro138Ala missense_variant 0.22
fbiB 3640965 c.-570C>G upstream_gene_variant 0.22
fbiB 3641622 p.Ser30Gly missense_variant 0.12
fbiB 3641625 p.Ala31Ser missense_variant 0.12
fbiB 3641848 p.Ala105Asp missense_variant 0.12
alr 3841516 c.-96G>T upstream_gene_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.31
rpoA 3877588 p.Ser307* stop_gained 0.13
rpoA 3878639 c.-132C>G upstream_gene_variant 0.4
clpC1 4039055 c.1650C>T synonymous_variant 0.12
clpC1 4039447 p.Asp420Tyr missense_variant 0.18
clpC1 4039730 c.975C>G synonymous_variant 0.13
panD 4044225 p.Asp19Glu missense_variant 0.15
embC 4242149 p.Ala763Thr missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244184 p.Ser318Leu missense_variant 0.13
embA 4245368 c.2136T>A synonymous_variant 0.12
embB 4246544 p.Thr11Pro missense_variant 0.38
embB 4246548 p.Pro12Gln missense_variant 0.62
embB 4246555 c.42G>C synonymous_variant 0.88
embB 4246556 p.Ala15Pro missense_variant 0.86
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4246626 p.Phe38Ser missense_variant 0.18
embB 4247106 p.Pro198His missense_variant 0.22
embB 4247336 p.Thr275Ser missense_variant 0.4
embB 4249051 c.2538C>A synonymous_variant 0.15
ethA 4326587 p.Val296Ala missense_variant 0.13
ethR 4326961 c.-588G>C upstream_gene_variant 0.14
ethR 4326964 c.-585G>A upstream_gene_variant 0.14
ethR 4326970 c.-579G>T upstream_gene_variant 0.15
ethA 4327334 p.Leu47* stop_gained 0.15
ethA 4327529 c.-56T>C upstream_gene_variant 0.17
ethA 4327845 c.-372G>C upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0