TB-Profiler result

Run: ERR233350
Summary

Run ID: ERR233350

Sample name:

Date: 13-08-2022 03:13:46

Number of reads: 8356487

Percentage reads mapped: 96.13

Strain: lineage4.2.2.2

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
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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.Lys88Thr missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Ala missense_variant 0.97 ethambutol
ethA 4327054 p.Tyr140* stop_gained 0.13 ethionamide
gid 4407997 p.Gly69Asp missense_variant 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.21
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7655 c.354G>C synonymous_variant 0.18
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoC 762836 c.-534C>G upstream_gene_variant 0.17
rpoC 764725 p.Phe452Leu missense_variant 0.18
rpoC 764751 p.Val461Gly missense_variant 0.23
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.19
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.18
fabG1 1673449 p.Thr4Pro missense_variant 0.28
inhA 1674892 p.Asn231Asp missense_variant 0.16
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.17
PPE35 2167871 c.2742G>C synonymous_variant 0.2
PPE35 2169379 p.Phe412Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290023 c.-782A>C upstream_gene_variant 0.27
kasA 2518891 c.777C>A synonymous_variant 0.16
eis 2714366 p.Val323Leu missense_variant 0.22
ahpC 2725954 c.-239C>T upstream_gene_variant 0.2
ahpC 2726146 c.-47_-46insT upstream_gene_variant 1.0
ahpC 2726756 c.564C>G synonymous_variant 0.17
folC 2746186 c.1413G>C synonymous_variant 0.18
ribD 2987392 p.Arg185Pro missense_variant 0.14
Rv2752c 3064552 p.Arg547Pro missense_variant 0.12
Rv2752c 3064741 p.Gly484Ala missense_variant 0.17
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339550 p.Gly145Trp missense_variant 0.19
Rv3083 3448929 p.Tyr142* stop_gained 0.13
Rv3083 3449673 p.Tyr390* stop_gained 0.23
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474601 p.Arg199Gly missense_variant 0.2
fprA 3475280 p.Val425Gly missense_variant 0.21
fbiB 3641955 p.Gly141Arg missense_variant 0.26
alr 3840268 p.Thr385Pro missense_variant 0.16
alr 3841504 c.-84C>G upstream_gene_variant 0.14
rpoA 3877766 p.Ala248Pro missense_variant 0.19
ddn 3987013 p.Gly57Ala missense_variant 0.23
clpC1 4039680 p.Phe342Ser missense_variant 0.2
clpC1 4039932 p.Gly258Val missense_variant 0.35
embC 4241056 c.1194C>G synonymous_variant 0.23
embC 4241456 p.Ala532Pro missense_variant 0.24
embC 4242476 p.Pro872Ala missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.2
embA 4243246 p.Gly5Val missense_variant 1.0
embA 4244375 c.1143C>G synonymous_variant 0.18
embB 4248725 p.Ser738Ala missense_variant 0.19
ethA 4327472 c.2T>G start_lost 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0