TB-Profiler result

Run: ERR2229630

Summary

Run ID: ERR2229630

Sample name:

Date: 31-03-2023 17:22:36

Number of reads: 586958

Percentage reads mapped: 99.06

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 5889 p.Glu217Val missense_variant 0.13
gyrB 6514 p.Glu425Asp missense_variant 0.14
gyrB 6803 p.Leu522Met missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7698 c.397C>A synonymous_variant 0.33
gyrA 7718 p.Met139Ile missense_variant 0.33
gyrA 8125 p.Pro275Leu missense_variant 0.12
gyrA 8721 p.Arg474Trp missense_variant 0.33
fgd1 490947 c.165G>A synonymous_variant 0.2
mshA 575571 p.Ser75Ile missense_variant 0.2
mshA 575963 p.Val206Phe missense_variant 0.17
ccsA 620137 p.Val83Phe missense_variant 0.4
ccsA 620765 p.Ala292Asp missense_variant 0.14
rpoB 760803 p.Val333Met missense_variant 0.14
rpoB 760862 c.1056G>T synonymous_variant 0.2
rpoB 760869 p.Val355Phe missense_variant 0.18
rpoB 761152 p.Leu449Gln missense_variant 0.22
rpoB 761958 p.Met718Val missense_variant 0.15
rpoC 765124 c.1755G>T synonymous_variant 0.25
rpoC 766852 p.Met1161Ile missense_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775726 c.2755C>T synonymous_variant 0.17
mmpL5 775727 c.2754C>G synonymous_variant 0.15
mmpL5 775914 p.Ala856Val missense_variant 0.25
mmpL5 775954 c.2527C>T synonymous_variant 0.15
mmpL5 775957 p.Ile842Val missense_variant 0.15
mmpL5 775964 p.Ala839Ser missense_variant 0.15
mmpL5 776514 p.His656Arg missense_variant 0.12
mmpL5 777119 p.His454Gln missense_variant 0.27
mmpL5 777122 c.1359C>T synonymous_variant 0.33
mmpL5 777128 c.1353A>G synonymous_variant 0.33
mmpL5 777157 c.1324C>A synonymous_variant 0.15
mmpL5 777164 c.1317C>T synonymous_variant 0.17
mmpR5 778340 c.-650G>A upstream_gene_variant 0.25
mmpL5 778913 c.-433G>T upstream_gene_variant 0.2
mmpR5 779360 p.Ala124Glu missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800902 p.Gly32Arg missense_variant 0.22
rplC 801435 c.627C>A synonymous_variant 0.15
fbiC 1302741 c.-190G>A upstream_gene_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406122 p.Pro407Thr missense_variant 0.22
Rv1258c 1406668 c.673T>C synonymous_variant 0.25
Rv1258c 1406926 p.Leu139Met missense_variant 0.18
Rv1258c 1407045 p.Asp99Gly missense_variant 0.25
embR 1416470 p.His293Pro missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472359 n.514A>G non_coding_transcript_exon_variant 0.4
rrs 1472417 n.572G>A non_coding_transcript_exon_variant 0.2
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
fabG1 1673380 c.-60C>G upstream_gene_variant 0.14
fabG1 1673618 p.Cys60Tyr missense_variant 0.22
fabG1 1673654 p.Phe72Ser missense_variant 0.22
fabG1 1673900 p.Ala154Val missense_variant 0.18
rpsA 1833552 p.Pro4Arg missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918643 p.Gly235Val missense_variant 0.15
ndh 2101819 p.Lys408Asn missense_variant 0.25
katG 2155338 p.Asn258Lys missense_variant 0.25
katG 2155456 p.Pro219Leu missense_variant 0.18
katG 2155990 p.Asn41Ser missense_variant 0.15
katG 2156543 c.-432G>C upstream_gene_variant 0.11
PPE35 2167686 p.Asn976Thr missense_variant 0.18
PPE35 2167695 p.Ile973Thr missense_variant 0.22
PPE35 2167745 p.Thr956Arg missense_variant 0.2
PPE35 2167814 c.2799C>T synonymous_variant 0.2
PPE35 2167833 p.Leu927Arg missense_variant 0.18
PPE35 2167865 c.2748G>C synonymous_variant 0.17
PPE35 2167868 c.2745A>C synonymous_variant 0.18
PPE35 2168140 p.Ala825Thr missense_variant 0.2
PPE35 2168143 p.Phe824Leu missense_variant 0.2
PPE35 2168150 c.2463T>C synonymous_variant 0.2
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169141 p.Thr491Lys missense_variant 0.13
PPE35 2169488 c.1125G>C synonymous_variant 0.14
PPE35 2169570 p.Ser348Asn missense_variant 0.16
PPE35 2169602 c.1011C>A synonymous_variant 0.24
PPE35 2169628 p.Ile329Val missense_variant 0.11
PPE35 2169629 c.984T>C synonymous_variant 0.11
PPE35 2169632 p.Ala327Gly missense_variant 0.12
PPE35 2169638 c.975T>C synonymous_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.23
PPE35 2170048 p.Leu189Val missense_variant 0.64
PPE35 2170053 p.Thr187Ser missense_variant 0.66
PPE35 2170147 p.Ser156Ala missense_variant 0.23
Rv1979c 2222458 p.Glu236Val missense_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518809 p.Lys232Arg missense_variant 0.2
kasA 2519052 p.Thr313Met missense_variant 0.18
kasA 2519140 c.1026G>C synonymous_variant 0.38
kasA 2519143 c.1029G>C synonymous_variant 0.38
eis 2714448 p.Trp295Cys missense_variant 0.67
eis 2715531 c.-199C>T upstream_gene_variant 0.33
pepQ 2859303 c.1116G>A synonymous_variant 0.18
ribD 2987365 p.Ala176Glu missense_variant 0.17
ribD 2987436 p.Gly200Trp missense_variant 0.18
Rv2752c 3065216 p.Ile326Val missense_variant 0.5
Rv2752c 3065401 p.Arg264Pro missense_variant 0.15
thyX 3067758 p.His63Leu missense_variant 0.22
thyA 3074175 c.297A>T synonymous_variant 0.67
thyA 3074413 p.Asp20Gly missense_variant 0.29
ald 3086640 c.-180T>A upstream_gene_variant 0.4
fbiD 3339588 c.471G>T synonymous_variant 0.25
fbiD 3339645 c.528C>T synonymous_variant 0.29
fprA 3474806 p.Met267Thr missense_variant 0.2
fprA 3475335 p.Lys443Asn missense_variant 0.29
Rv3236c 3612957 p.Ala54Thr missense_variant 0.22
fbiB 3642047 c.513G>C synonymous_variant 0.5
fbiB 3642765 p.Glu411* stop_gained 0.15
alr 3840473 p.Asp316Glu missense_variant 0.2
alr 3840483 p.Gly313Val missense_variant 0.18
alr 3841247 p.His58Gln missense_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.33
alr 3841612 c.-193_-192insC upstream_gene_variant 0.26
rpoA 3878168 p.Ala114Thr missense_variant 0.33
clpC1 4038281 p.Asp808Glu missense_variant 0.33
clpC1 4039645 p.His354Asp missense_variant 0.18
clpC1 4039654 p.Thr351Ser missense_variant 0.13
clpC1 4039691 c.1014G>C synonymous_variant 0.13
clpC1 4039714 p.Tyr331His missense_variant 0.18
clpC1 4040144 c.561G>C synonymous_variant 0.33
embC 4239864 c.2T>C start_lost 0.18
embC 4240694 p.Ile278Val missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244414 c.1182G>T synonymous_variant 0.22
embA 4246035 p.Glu935* stop_gained 0.29
embB 4246548 p.Pro12Gln missense_variant 0.43
embB 4246555 c.42G>C synonymous_variant 0.56
embB 4246556 p.Ala15Pro missense_variant 0.56
embB 4246563 p.Leu17Trp missense_variant 0.5
embB 4246567 c.54_55insT frameshift_variant 0.25
embB 4246879 c.366C>A synonymous_variant 0.29
embB 4246904 p.Val131Leu missense_variant 0.22
embB 4247426 p.Gly305Thr missense_variant 0.4
embB 4247470 c.957T>C synonymous_variant 0.25
embB 4247472 p.Phe320Tyr missense_variant 0.25
embB 4248055 c.1542G>T synonymous_variant 0.18
embB 4248401 p.Ala630Ser missense_variant 0.14
embB 4248636 p.Pro708Leu missense_variant 0.4
embB 4248862 c.2349C>T synonymous_variant 0.18
embB 4249034 c.2521C>A synonymous_variant 0.25
embB 4249040 p.Pro843Thr missense_variant 0.25
embB 4249088 p.Val859Phe missense_variant 0.18
embB 4249248 p.Pro912His missense_variant 0.25
aftB 4267087 p.Leu584Met missense_variant 0.15
aftB 4267406 p.Lys477His missense_variant 0.18
aftB 4267411 p.Gly476Cys missense_variant 0.18
aftB 4267413 p.Gly475Ala missense_variant 0.18
ethA 4326153 p.Arg441Ser missense_variant 0.17
ethA 4326503 p.Gly324Val missense_variant 0.17
ethR 4327219 c.-330G>T upstream_gene_variant 0.15
ethA 4327257 p.Gln73Lys missense_variant 0.14
ethA 4327614 c.-141G>C upstream_gene_variant 0.12
whiB6 4338384 c.138C>T synonymous_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407732 c.471G>A synonymous_variant 0.2
gid 4408471 c.-269G>C upstream_gene_variant 0.22
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0