TB-Profiler result

Run: ERR2229686
Summary

Run ID: ERR2229686

Sample name:

Date: 31-03-2023 17:26:21

Number of reads: 850303

Percentage reads mapped: 99.26

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 6005 p.Gly256Cys missense_variant 0.15
gyrB 6207 p.Ala323Val missense_variant 0.12
gyrB 6603 p.Leu455Pro missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8165 c.864C>T synonymous_variant 0.12
gyrA 8731 p.Gly477Ala missense_variant 0.4
mshA 576108 p.Ala254Gly missense_variant 0.19
mshA 576482 p.Val379Ile missense_variant 0.29
mshA 576769 c.1423delC frameshift_variant 0.14
ccsA 620169 c.279G>A synonymous_variant 0.12
rpoB 760549 p.Phe248Ser missense_variant 0.2
rpoB 762802 p.Asp999Val missense_variant 0.22
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778249 p.Ile78Phe missense_variant 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781604 c.45G>A synonymous_variant 0.2
rplC 801208 p.Gly134Ser missense_variant 0.17
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1303909 p.Pro327Ser missense_variant 0.22
Rv1258c 1406788 p.Ile185Val missense_variant 0.11
embR 1416554 p.Ser265Tyr missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1673357 c.-83G>A upstream_gene_variant 0.17
fabG1 1673359 c.-81T>C upstream_gene_variant 0.18
fabG1 1673361 c.-79C>G upstream_gene_variant 0.18
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
inhA 1673985 c.-217C>T upstream_gene_variant 0.18
inhA 1675004 p.Leu268Ser missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2153970 p.Asp714Glu missense_variant 0.17
katG 2154693 c.1419T>A synonymous_variant 0.13
katG 2155344 c.768C>T synonymous_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169052 p.Asn521Asp missense_variant 0.17
PPE35 2169382 p.Trp411Gly missense_variant 0.22
PPE35 2169383 c.1230C>G synonymous_variant 0.17
PPE35 2169394 p.Ala407Thr missense_variant 0.18
PPE35 2169396 p.Gly406Asp missense_variant 0.18
PPE35 2170035 p.Val193Ala missense_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.65
PPE35 2170053 p.Thr187Ser missense_variant 0.65
PPE35 2170189 p.Glu142Gln missense_variant 0.11
PPE35 2170190 c.423G>A synonymous_variant 0.11
PPE35 2170513 c.100C>T synonymous_variant 0.12
Rv1979c 2222447 p.Asn240Asp missense_variant 0.13
Rv1979c 2223020 c.143_144dupCG frameshift_variant 0.14
Rv1979c 2223131 p.His12Tyr missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290029 c.-788G>T upstream_gene_variant 0.14
kasA 2518499 p.Met129Leu missense_variant 0.15
kasA 2518843 c.729T>G synonymous_variant 0.17
eis 2715541 c.-209A>T upstream_gene_variant 0.2
folC 2746146 p.Asp485His missense_variant 0.12
folC 2746943 p.Ile219Thr missense_variant 0.2
pepQ 2860328 c.91C>A synonymous_variant 0.18
Rv2752c 3065571 p.Glu207Asp missense_variant 0.12
thyX 3067340 c.606G>A synonymous_variant 0.13
thyX 3067344 c.601delA frameshift_variant 0.15
thyA 3074556 c.-85T>C upstream_gene_variant 0.12
whiB7 3568402 c.278A>G stop_lost&splice_region_variant 0.14
whiB7 3568736 c.-57T>C upstream_gene_variant 0.17
fbiA 3640870 p.Ala110Ser missense_variant 0.14
fbiA 3640892 p.Gln117Arg missense_variant 0.15
fbiB 3641553 p.Gly7Arg missense_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.21
ddn 3987004 c.162delC frameshift_variant 0.25
clpC1 4038822 p.Glu628Gly missense_variant 0.12
clpC1 4038964 p.Asp581Tyr missense_variant 0.12
panD 4044332 c.-51C>T upstream_gene_variant 0.2
embC 4241421 p.Glu520Val missense_variant 0.13
embC 4242621 p.Val920Asp missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243517 c.285C>T synonymous_variant 0.2
embA 4246396 c.3165_3166delAT frameshift_variant 0.14
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4246555 c.42G>C synonymous_variant 0.47
embB 4246556 p.Ala15Pro missense_variant 0.53
embB 4246563 p.Leu17Trp missense_variant 0.33
embB 4246567 c.54G>T synonymous_variant 0.33
embB 4247026 c.513G>C synonymous_variant 0.22
embB 4247636 p.Pro375Thr missense_variant 0.15
aftB 4268121 p.Thr239Asn missense_variant 0.12
ubiA 4269572 p.Arg88Gly missense_variant 0.11
ethR 4327696 p.Leu50Met missense_variant 0.22
whiB6 4338513 p.Tyr3* stop_gained 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0