TB-Profiler result

Run: ERR7910942
Summary

Run ID: ERR7910942

Sample name:

Date: 02-04-2023 06:36:21

Number of reads: 345228

Percentage reads mapped: 99.48

Strain: lineage4.2.1

Drug-resistance: MDR-TB

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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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 None 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2154970 p.Asp381Gly missense_variant 0.5 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247402 p.Ser297Ala missense_variant 1.0 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
gyrB 5678 p.Ser147Ala missense_variant 0.29
gyrB 5696 p.Ser153Ala missense_variant 0.33
gyrB 6600 p.Glu454Val missense_variant 0.22
gyrB 6972 p.Pro578Gln missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7666 p.Asp122Ala missense_variant 0.43
gyrA 8399 c.1098T>A synonymous_variant 0.25
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9784 p.Val828Ala missense_variant 0.33
fgd1 490696 c.-87T>G upstream_gene_variant 0.18
fgd1 490800 c.18A>T synonymous_variant 0.2
fgd1 490850 p.Leu23Gln missense_variant 0.14
fgd1 490962 c.180T>C synonymous_variant 0.2
fgd1 490981 p.Arg67Gly missense_variant 0.15
fgd1 491247 c.465C>T synonymous_variant 1.0
mshA 576500 p.Ile385Val missense_variant 0.29
ccsA 619958 p.Val23Ala missense_variant 0.29
ccsA 619969 p.Val27Ile missense_variant 1.0
ccsA 620132 p.Leu81Pro missense_variant 0.25
ccsA 620865 c.975A>C stop_lost&splice_region_variant 0.2
rpoB 759859 p.Pro18Leu missense_variant 0.25
rpoC 762419 c.-951C>A upstream_gene_variant 0.2
rpoB 762594 p.Leu930Met missense_variant 0.18
rpoB 762793 p.Val996Gly missense_variant 0.25
rpoB 763285 p.Leu1160Gln missense_variant 0.38
rpoC 763511 p.Cys48Ser missense_variant 0.22
rpoC 764817 p.Val483Gly missense_variant 1.0
rpoC 765076 c.1707A>G synonymous_variant 0.25
rpoC 766481 c.3112C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777258 p.Leu408Gln missense_variant 0.2
mmpL5 777473 c.1008T>C synonymous_variant 0.33
mmpL5 778072 p.Thr137Pro missense_variant 0.2
mmpL5 778078 p.Thr135Pro missense_variant 0.45
mmpR5 778226 c.-764T>A upstream_gene_variant 0.18
mmpL5 778256 p.Met75Ile missense_variant 0.17
mmpL5 778441 p.Pro14Thr missense_variant 0.22
mmpS5 779659 c.-754T>A upstream_gene_variant 0.33
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781460 c.-100A>T upstream_gene_variant 0.25
rpsL 781547 c.-13A>T upstream_gene_variant 0.29
Rv1258c 1407538 c.-198T>A upstream_gene_variant 0.25
embR 1416440 p.Leu303Gln missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471814 n.-32T>G upstream_gene_variant 0.8
rrs 1472002 n.157A>G non_coding_transcript_exon_variant 0.14
rrs 1472888 n.1043T>C non_coding_transcript_exon_variant 0.4
rrs 1473192 n.1347A>T non_coding_transcript_exon_variant 0.17
rrl 1475472 n.1815T>A non_coding_transcript_exon_variant 0.29
fabG1 1673820 p.Met127Ile missense_variant 0.33
rpsA 1833949 c.408T>C synonymous_variant 0.25
rpsA 1834490 p.Ile317Phe missense_variant 0.29
rpsA 1834664 p.Pro375Thr missense_variant 0.29
tlyA 1917872 c.-68T>G upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918490 p.Gln184Leu missense_variant 0.2
ndh 2102135 p.Val303Gly missense_variant 0.17
katG 2154326 p.Asn596Tyr missense_variant 0.33
PPE35 2169029 p.Asp528Glu missense_variant 0.33
PPE35 2169703 p.Asn304Tyr missense_variant 0.4
PPE35 2169879 p.Phe245Cys missense_variant 1.0
PPE35 2170490 c.123T>C synonymous_variant 0.17
Rv1979c 2221727 p.Thr480Ser missense_variant 0.27
Rv1979c 2222633 p.Ile178Phe missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715111 p.Glu74Asp missense_variant 0.25
ahpC 2726722 p.Asn177Thr missense_variant 0.33
pepQ 2859390 c.1029A>T synonymous_variant 0.4
pepQ 2859639 c.780T>G synonymous_variant 0.27
Rv2752c 3064677 p.Glu505Asp missense_variant 0.4
Rv2752c 3065088 c.1104A>T synonymous_variant 0.5
Rv2752c 3065541 p.Glu217Asp missense_variant 0.29
thyX 3067749 p.Asp66Val missense_variant 0.67
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087278 p.Gln153His missense_variant 0.29
ald 3087787 p.Glu323Gly missense_variant 0.25
ald 3087822 p.Ser335Pro missense_variant 0.33
Rv3083 3449555 p.Gln351Leu missense_variant 0.22
Rv3083 3449807 p.Met435Thr missense_variant 0.29
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474971 p.Val322Gly missense_variant 0.2
whiB7 3568428 c.252A>G synonymous_variant 0.33
whiB7 3568754 c.-75T>A upstream_gene_variant 0.5
Rv3236c 3612000 p.Thr373Ser missense_variant 0.29
Rv3236c 3612508 c.609T>G synonymous_variant 0.5
Rv3236c 3613095 p.Leu8Val missense_variant 0.4
fbiB 3642717 p.Ser395Cys missense_variant 0.29
alr 3840306 p.Gly372Asp missense_variant 0.13
alr 3840588 p.Lys278Ile missense_variant 0.38
alr 3841079 p.His114Gln missense_variant 0.22
alr 3841551 c.-131G>C upstream_gene_variant 0.25
rpoA 3877852 p.Phe219Ser missense_variant 0.2
rpoA 3878458 p.Asn17Thr missense_variant 0.5
clpC1 4038592 p.Phe705Leu missense_variant 0.29
clpC1 4038993 p.Phe571Ser missense_variant 0.33
clpC1 4039443 p.Leu421Gln missense_variant 0.2
clpC1 4040031 p.Val225Gly missense_variant 0.38
clpC1 4040067 p.Val213Ala missense_variant 0.4
clpC1 4040249 p.Glu152Asp missense_variant 0.4
embC 4240025 p.Thr55Pro missense_variant 0.29
embC 4241248 c.1386G>C synonymous_variant 0.18
embC 4241309 p.Thr483Pro missense_variant 0.29
embC 4241657 p.Ser599Ala missense_variant 0.29
embC 4241925 p.Arg688Leu missense_variant 0.2
embC 4241971 c.2109T>A synonymous_variant 0.22
embC 4242170 p.Thr770Pro missense_variant 0.2
embC 4242212 c.2352delC frameshift_variant 0.2
embC 4242245 p.Thr795Pro missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246189 p.Asn986Thr missense_variant 0.33
embA 4246326 p.Phe1032Ile missense_variant 0.18
embB 4249594 c.3081G>A synonymous_variant 1.0
aftB 4268619 p.Val73Gly missense_variant 0.33
aftB 4268714 c.123A>T synonymous_variant 0.25
aftB 4268826 p.Val4Gly missense_variant 0.75
ubiA 4269307 p.Phe176Cys missense_variant 1.0
ubiA 4269716 p.Leu40Val missense_variant 0.4
ethA 4326632 p.His281Pro missense_variant 1.0
ethR 4328041 p.Thr165Pro missense_variant 0.25
ethA 4328376 c.-903G>C upstream_gene_variant 0.95
whiB6 4338528 c.-7A>T upstream_gene_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408283 c.-81A>C upstream_gene_variant 0.14