TB-Profiler result

Run: ERR2229631
Summary

Run ID: ERR2229631

Sample name:

Date: 31-03-2023 17:22:38

Number of reads: 673886

Percentage reads mapped: 99.21

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 6263 p.Asp342Asn missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 8702 c.1402_1403delAT frameshift_variant 0.17
fgd1 491207 p.Leu142Pro missense_variant 0.17
fgd1 491408 p.Pro209Gln missense_variant 0.2
mshA 575490 p.Ala48Gly missense_variant 0.13
mshA 576108 p.Ala254Gly missense_variant 0.29
mshA 576705 p.Gln453Leu missense_variant 0.12
ccsA 619973 c.94_96delCTG conservative_inframe_deletion 0.4
rpoB 761773 p.His656Arg missense_variant 0.14
rpoC 762764 c.-606G>T upstream_gene_variant 0.18
rpoC 763079 c.-291C>T upstream_gene_variant 0.12
rpoC 764133 p.Ala255Val missense_variant 0.29
rpoC 765674 p.Glu769Lys missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776354 c.2126delT frameshift_variant 0.18
mmpL5 776712 p.His590Leu missense_variant 0.18
mmpL5 777113 p.Met456Ile missense_variant 0.14
mmpL5 778083 p.Pro133Leu missense_variant 0.17
mmpL5 778113 p.Val123Ala missense_variant 0.22
mmpL5 778239 p.Val81Gly missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303747 p.Thr273Ala missense_variant 1.0
fbiC 1304817 p.His629Gln missense_variant 0.22
Rv1258c 1407316 p.Ala9Thr missense_variant 0.22
Rv1258c 1407462 c.-122A>G upstream_gene_variant 0.13
embR 1416424 c.924C>A synonymous_variant 0.13
embR 1416551 p.Ala266Val missense_variant 0.15
embR 1416924 p.Leu142Met missense_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475062 n.1405A>G non_coding_transcript_exon_variant 0.17
rrl 1475992 n.2335T>A non_coding_transcript_exon_variant 0.12
rrl 1476145 n.2488G>T non_coding_transcript_exon_variant 0.12
fabG1 1673764 p.Ile109Phe missense_variant 0.2
inhA 1674558 c.357C>T synonymous_variant 0.22
rpsA 1833557 p.Val6Ile missense_variant 0.33
rpsA 1833984 p.Leu148Pro missense_variant 0.2
rpsA 1834638 p.Asn366Ser missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101991 p.Leu351Gln missense_variant 0.14
ndh 2102912 p.Ala44Val missense_variant 0.33
katG 2153943 c.2169C>T synonymous_variant 0.13
katG 2155641 c.471G>A synonymous_variant 0.12
katG 2156014 p.Gly33Val missense_variant 0.25
PPE35 2167745 p.Thr956Arg missense_variant 0.22
PPE35 2167965 p.Ala883Gly missense_variant 0.15
PPE35 2167967 c.2646A>C synonymous_variant 0.15
PPE35 2168140 p.Ala825Thr missense_variant 0.17
PPE35 2168143 p.Phe824Leu missense_variant 0.17
PPE35 2168150 c.2463T>C synonymous_variant 0.18
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168981 c.1632A>T synonymous_variant 0.25
PPE35 2169109 p.Asp502Tyr missense_variant 0.2
PPE35 2169278 c.1335T>C synonymous_variant 0.12
PPE35 2169281 c.1332T>G synonymous_variant 0.13
PPE35 2169748 p.Ile289Phe missense_variant 0.17
PPE35 2169749 c.864A>C synonymous_variant 0.17
PPE35 2169902 c.711G>C synonymous_variant 0.19
PPE35 2170048 p.Leu189Val missense_variant 0.55
PPE35 2170053 p.Thr187Ser missense_variant 0.56
PPE35 2170147 p.Ser156Ala missense_variant 0.26
PPE35 2170403 c.210C>G synonymous_variant 0.14
Rv1979c 2222359 p.Leu269Pro missense_variant 0.11
Rv1979c 2222407 p.Pro253Leu missense_variant 0.12
Rv1979c 2223287 c.-123G>C upstream_gene_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290028 c.-787C>A upstream_gene_variant 0.15
pncA 2290111 c.-870G>A upstream_gene_variant 0.12
kasA 2518879 c.765A>G synonymous_variant 0.3
kasA 2518882 c.768C>A synonymous_variant 0.29
kasA 2519057 p.Thr315Ser missense_variant 0.14
kasA 2519062 c.948T>G synonymous_variant 0.17
kasA 2519065 c.951C>A synonymous_variant 0.18
kasA 2519070 p.Asp319Val missense_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.2
kasA 2519143 c.1029G>C synonymous_variant 0.22
ahpC 2726489 c.297G>A synonymous_variant 0.14
ribD 2986949 c.111C>T synonymous_variant 0.12
ribD 2987580 p.Ser248Thr missense_variant 0.14
Rv2752c 3064980 c.1212C>A synonymous_variant 0.2
Rv2752c 3066132 c.60G>A synonymous_variant 0.17
thyX 3067966 c.-21G>T upstream_gene_variant 0.12
ald 3086625 c.-195G>T upstream_gene_variant 0.19
Rv3083 3448472 c.-32A>T upstream_gene_variant 0.25
fprA 3474002 c.-5C>A upstream_gene_variant 0.2
fprA 3474999 c.993G>C synonymous_variant 0.2
whiB7 3568428 c.252A>G synonymous_variant 0.29
Rv3236c 3613238 c.-122C>G upstream_gene_variant 0.17
alr 3841129 c.292C>T synonymous_variant 0.15
alr 3841147 p.Ala92Ser missense_variant 0.18
alr 3841546 c.-126C>A upstream_gene_variant 0.59
rpoA 3877946 p.Asp188Tyr missense_variant 0.18
rpoA 3878377 p.Ser44Leu missense_variant 0.13
clpC1 4039042 p.Ser555Thr missense_variant 0.17
clpC1 4039645 p.His354Asp missense_variant 0.24
clpC1 4039654 p.Thr351Ser missense_variant 0.36
clpC1 4039829 p.Leu292Phe missense_variant 0.13
clpC1 4040144 c.561G>C synonymous_variant 0.38
clpC1 4040373 p.Gly111Asp missense_variant 0.14
panD 4044202 p.Thr27Asn missense_variant 0.33
embC 4240760 p.Met300Leu missense_variant 0.13
embC 4242207 p.Ser782Cys missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244741 p.Tyr503* stop_gained 0.25
embA 4246464 p.Val1078Leu missense_variant 0.22
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4246555 c.42G>C synonymous_variant 0.43
embB 4246556 p.Ala15Pro missense_variant 0.43
embB 4246810 c.297G>A synonymous_variant 0.14
embB 4248668 p.Val719Ile missense_variant 0.2
embB 4249241 p.Leu910Met missense_variant 0.15
embB 4249257 p.Arg915Gln missense_variant 0.12
embB 4249716 p.Asp1068Val missense_variant 0.38
ethA 4326369 p.Tyr369Asp missense_variant 0.13
ethA 4327538 c.-65T>C upstream_gene_variant 0.11
ethA 4328151 c.-678A>G upstream_gene_variant 0.12
ethA 4328367 c.-894C>T upstream_gene_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407814 p.Gly130Val missense_variant 0.15
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0