TB-Profiler result

Run: ERR2229383
Summary

Run ID: ERR2229383

Sample name:

Date: 31-03-2023 17:08:07

Number of reads: 889168

Percentage reads mapped: 98.91

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 6134 p.Glu299* stop_gained 0.27
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9359 c.2058C>T synonymous_variant 0.13
mshA 575740 c.393G>T synonymous_variant 0.12
mshA 576108 p.Ala254Gly missense_variant 0.25
rpoB 759860 c.54G>C synonymous_variant 0.2
rpoB 761211 p.Val469Leu missense_variant 0.18
rpoB 761796 p.Tyr664Asn missense_variant 0.12
rpoC 765216 p.Ala616Asp missense_variant 0.29
rpoC 765258 p.Arg630Leu missense_variant 0.25
rpoC 765988 c.2619G>A synonymous_variant 0.2
rpoC 766659 p.Arg1097Leu missense_variant 0.18
rpoC 766714 c.3345G>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777128 c.1353A>G synonymous_variant 0.15
mmpR5 778049 c.-941G>T upstream_gene_variant 0.18
mmpL5 778170 p.Ala104Val missense_variant 0.25
mmpS5 778758 p.Pro50Ala missense_variant 0.2
mmpL5 778913 c.-433G>T upstream_gene_variant 0.14
mmpS5 779495 c.-590G>T upstream_gene_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304578 p.Arg550Ser missense_variant 0.12
fbiC 1304893 p.Gly655Ser missense_variant 0.12
fbiC 1305025 p.Glu699* stop_gained 0.13
Rv1258c 1406374 p.Leu323Met missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474085 n.428A>G non_coding_transcript_exon_variant 0.11
rrl 1474157 n.500G>T non_coding_transcript_exon_variant 0.12
fabG1 1673359 c.-81T>C upstream_gene_variant 0.11
fabG1 1673361 c.-79C>G upstream_gene_variant 0.11
fabG1 1673380 c.-60C>G upstream_gene_variant 0.35
fabG1 1673549 p.Ala37Val missense_variant 0.22
inhA 1674087 c.-115G>A upstream_gene_variant 0.18
inhA 1674785 p.Arg195Leu missense_variant 0.29
rpsA 1833724 c.183C>T synonymous_variant 0.17
rpsA 1834363 p.Leu274Phe missense_variant 0.22
rpsA 1834422 p.Gly294Glu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101852 c.1191G>T synonymous_variant 0.12
ndh 2101981 c.1062C>A synonymous_variant 0.18
ndh 2102044 c.999G>T synonymous_variant 0.17
katG 2155230 p.Glu294Asp missense_variant 0.2
PPE35 2167732 p.Phe961Val missense_variant 0.29
PPE35 2167746 p.Thr956Ser missense_variant 0.2
PPE35 2167973 c.2640A>G synonymous_variant 0.19
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169281 c.1332T>G synonymous_variant 0.13
PPE35 2169287 c.1326T>C synonymous_variant 0.16
PPE35 2169902 c.711G>C synonymous_variant 0.13
PPE35 2170048 p.Leu189Val missense_variant 0.7
PPE35 2170053 p.Thr187Ser missense_variant 0.76
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289398 c.-157G>A upstream_gene_variant 0.13
kasA 2518829 p.Phe239Ile missense_variant 0.17
kasA 2518879 c.765A>G synonymous_variant 0.17
kasA 2518882 c.768C>A synonymous_variant 0.2
kasA 2519140 c.1026G>C synonymous_variant 0.25
kasA 2519143 c.1029G>C synonymous_variant 0.25
kasA 2519153 p.Ile347Val missense_variant 0.25
eis 2714599 c.733delA frameshift_variant 0.2
ahpC 2725970 c.-223G>A upstream_gene_variant 0.12
folC 2746996 p.His201Gln missense_variant 0.12
pepQ 2859570 p.Asp283Glu missense_variant 0.22
pepQ 2859740 p.Ala227Ser missense_variant 0.2
pepQ 2859811 p.Pro203Leu missense_variant 0.15
ribD 2986673 c.-166C>A upstream_gene_variant 0.2
ribD 2987532 p.Gly232Arg missense_variant 0.12
Rv2752c 3066242 c.-51G>T upstream_gene_variant 0.22
Rv2752c 3066254 c.-63G>T upstream_gene_variant 0.29
thyX 3068015 c.-70T>G upstream_gene_variant 0.13
ald 3087559 p.Pro247His missense_variant 0.14
ald 3087726 p.Ala303Ser missense_variant 0.12
fprA 3474301 p.Ala99Ser missense_variant 0.18
fbiA 3640612 p.Gly24Ser missense_variant 0.17
fbiA 3641470 p.Met310Leu missense_variant 0.17
fbiB 3642303 p.Gln257Lys missense_variant 0.17
alr 3840677 c.744C>T synonymous_variant 0.13
clpC1 4038241 p.Gly822Arg missense_variant 0.4
clpC1 4038293 c.2412G>C synonymous_variant 0.22
clpC1 4038881 c.1824C>T synonymous_variant 0.12
clpC1 4039018 p.Ser563Ala missense_variant 0.15
clpC1 4039022 c.1683A>G synonymous_variant 0.17
clpC1 4039161 p.His515Gly missense_variant 0.2
clpC1 4039257 p.Gln483Arg missense_variant 0.14
clpC1 4039645 p.His354Asp missense_variant 0.17
clpC1 4039654 p.Thr351Ser missense_variant 0.13
clpC1 4039714 p.Tyr331His missense_variant 0.16
clpC1 4040144 c.561G>C synonymous_variant 0.2
clpC1 4040366 c.339C>T synonymous_variant 0.14
panD 4044063 c.219T>A synonymous_variant 0.15
panD 4044193 p.Ala30Asp missense_variant 0.15
embC 4240592 p.Ala244Ser missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242648 p.Leu929Arg missense_variant 0.33
embA 4244573 c.1341G>A synonymous_variant 0.29
embA 4244821 p.Gly530Val missense_variant 1.0
embB 4246555 c.42G>C synonymous_variant 0.5
embB 4246556 p.Ala15Pro missense_variant 0.5
embB 4246563 p.Leu17Trp missense_variant 0.67
embB 4246567 c.54G>T synonymous_variant 0.67
embB 4247470 c.957T>C synonymous_variant 0.29
embB 4247472 p.Phe320Tyr missense_variant 0.29
embB 4248589 c.2076C>A synonymous_variant 0.29
aftB 4268209 p.Arg210Cys missense_variant 0.17
aftB 4269351 c.-515C>G upstream_gene_variant 0.17
ubiA 4269548 p.Val96Leu missense_variant 0.2
ethR 4326955 c.-594G>A upstream_gene_variant 0.17
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethA 4327540 c.-67C>A upstream_gene_variant 0.13
ethA 4327809 c.-336T>C upstream_gene_variant 0.12
whiB6 4338204 c.318G>T synonymous_variant 0.15
whiB6 4338259 p.Arg88Gln missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407849 c.354C>T synonymous_variant 0.15
Rv3083 3448497 c.-6_*1408del transcript_ablation 1.0