TB-Profiler result

Run: ERR9806975
Summary

Run ID: ERR9806975

Sample name:

Date: 21-05-2023 06:38:34

Number of reads: 2038752

Percentage reads mapped: 99.31

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide
Streptomycin R rrs n.462C>T (0.19)
Fluoroquinolones R gyrA p.Asp94Ala (1.00)
Moxifloxacin R gyrA p.Asp94Ala (1.00)
Ofloxacin R gyrA p.Asp94Ala (1.00)
Levofloxacin R gyrA p.Asp94Ala (1.00)
Ciprofloxacin R gyrA p.Asp94Ala (1.00)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (1.00), ethR p.Ala95Thr (1.00)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.19 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethR 4327831 p.Ala95Thr missense_variant 1.0 ethionamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 7707 p.Pro136Thr missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490799 c.18delA frameshift_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759760 c.-47C>A upstream_gene_variant 0.12
rpoB 761099 c.1293C>T synonymous_variant 0.17
rpoB 761570 c.1764T>C synonymous_variant 0.14
rpoB 761573 c.1767C>G synonymous_variant 0.14
rpoB 761579 c.1773G>C synonymous_variant 0.14
rpoB 761606 c.1800C>G synonymous_variant 0.14
rpoB 761612 c.1806G>C synonymous_variant 0.16
rpoB 761615 c.1809A>C synonymous_variant 0.17
rpoB 761636 c.1830G>T synonymous_variant 0.19
rpoB 761645 c.1839C>G synonymous_variant 0.18
rpoB 761648 c.1842T>C synonymous_variant 0.18
rpoB 761657 c.1851C>G synonymous_variant 0.18
rpoB 761675 c.1869G>C synonymous_variant 0.16
rpoB 761690 c.1884G>C synonymous_variant 0.16
rpoB 761732 c.1926C>G synonymous_variant 0.12
rpoB 761735 c.1929C>G synonymous_variant 0.12
rpoB 761747 c.1941G>C synonymous_variant 0.11
rpoB 761750 c.1944G>C synonymous_variant 0.11
rpoB 762310 p.His835Arg missense_variant 1.0
rpoB 762688 p.Gln961Arg missense_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763555 c.186C>T synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778979 c.-74G>T upstream_gene_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800612 c.-197A>G upstream_gene_variant 0.27
rplC 800618 c.-191T>C upstream_gene_variant 0.27
rplC 800648 c.-161A>C upstream_gene_variant 0.29
rplC 800654 c.-155T>C upstream_gene_variant 0.25
rplC 800690 c.-119C>T upstream_gene_variant 0.21
rplC 800693 c.-116A>G upstream_gene_variant 0.2
rplC 800703 c.-106T>C upstream_gene_variant 0.17
rplC 800715 c.-94A>C upstream_gene_variant 0.15
rplC 800720 c.-89T>C upstream_gene_variant 0.14
rplC 801139 c.332delA frameshift_variant 0.13
Rv1258c 1406561 c.780G>T synonymous_variant 0.12
Rv1258c 1406656 p.Gly229Trp missense_variant 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406873 c.468C>A synonymous_variant 0.12
Rv1258c 1407215 c.126G>T synonymous_variant 0.13
Rv1258c 1407281 c.60C>T synonymous_variant 0.14
embR 1416344 p.Thr335Met missense_variant 0.15
embR 1416774 p.Ala192Thr missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472522 n.677T>A non_coding_transcript_exon_variant 0.11
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.16
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.16
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.16
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.2
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.19
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.14
rrl 1474427 n.770A>C non_coding_transcript_exon_variant 0.1
rrl 1474429 n.772G>C non_coding_transcript_exon_variant 0.1
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.23
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.15
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.23
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.14
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.18
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.13
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.12
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.12
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14
inhA 1674914 c.715_716dupGC frameshift_variant 0.15
rpsA 1833970 c.429G>C synonymous_variant 0.1
rpsA 1833979 c.438T>C synonymous_variant 0.11
rpsA 1834000 c.459G>C synonymous_variant 0.1
rpsA 1834015 c.474G>C synonymous_variant 0.11
rpsA 1834021 c.480C>T synonymous_variant 0.12
rpsA 1834097 c.556_557delTCinsAG synonymous_variant 0.13
rpsA 1834102 c.561T>C synonymous_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102052 p.Gly331Cys missense_variant 0.22
ndh 2102515 c.528C>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2222527 p.Ile213Thr missense_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289710 c.-469G>T upstream_gene_variant 0.13
eis 2714337 c.995delA frameshift_variant 0.12
eis 2714422 p.Ala304Val missense_variant 0.12
ribD 2987017 p.Gly60Val missense_variant 0.12
ribD 2987349 p.Gly171Ser missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339568 c.451C>T synonymous_variant 0.11
Rv3083 3449144 p.Pro214Gln missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568439 p.Arg81Cys missense_variant 0.17
Rv3236c 3612677 p.Glu147Gly missense_variant 0.11
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3840753 p.Arg223His missense_variant 0.11
rpoA 3878580 c.-74delC upstream_gene_variant 0.12
clpC1 4038671 c.2034T>C synonymous_variant 0.1
clpC1 4038695 c.2010C>G synonymous_variant 0.11
clpC1 4038701 c.2004G>C synonymous_variant 0.11
clpC1 4038704 c.2001T>C synonymous_variant 0.11
clpC1 4038707 c.1998C>G synonymous_variant 0.1
clpC1 4038710 c.1995G>C synonymous_variant 0.13
clpC1 4038713 c.1992T>C synonymous_variant 0.13
clpC1 4038740 c.1965G>C synonymous_variant 0.16
clpC1 4038755 c.1950G>C synonymous_variant 0.14
clpC1 4038773 c.1932T>C synonymous_variant 0.12
clpC1 4038782 c.1923G>C synonymous_variant 0.12
clpC1 4038790 c.1915C>T synonymous_variant 0.12
clpC1 4038812 c.1893T>C synonymous_variant 0.12
clpC1 4038815 c.1890G>T synonymous_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244324 c.1092T>C synonymous_variant 0.12
aftB 4267518 p.Thr440Ile missense_variant 0.13
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268012 c.825G>A synonymous_variant 0.17
aftB 4268478 p.Ala120Val missense_variant 0.11
ethA 4327143 p.Thr111Ser missense_variant 0.12
ethA 4327404 p.Gln24Lys missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0