TB-Profiler result

Run: ERR2514267
Summary

Run ID: ERR2514267

Sample name:

Date: 31-03-2023 20:13:48

Number of reads: 662847

Percentage reads mapped: 98.79

Strain: lineage2.2.1.2

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
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
lineage2.2.1.2 East-Asian (Beijing) Beijing-RD142 RD105;RD207;RD181;RD142 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
rpoC 764822 p.Asp485Asn missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288835 p.Asp136Gly missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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 5525 p.Val96Ile missense_variant 0.12
gyrB 6407 p.Glu390* stop_gained 0.12
gyrA 7313 c.12G>A synonymous_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8729 c.1431delG frameshift_variant 0.18
gyrA 8953 p.Gln551Arg missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9538 p.Gly746Asp missense_variant 0.2
gyrA 9552 p.Leu751Met missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575173 c.-175G>A upstream_gene_variant 0.67
mshA 575387 p.Ala14Ser missense_variant 0.15
mshA 575721 p.Leu125Pro missense_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576509 p.Thr388Ala missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761738 c.1932C>T synonymous_variant 0.14
rpoB 761800 p.Arg665Pro missense_variant 0.12
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763439 c.72delC frameshift_variant 0.17
rpoC 763707 p.Arg113Leu missense_variant 0.18
rpoC 766792 c.3423C>G synonymous_variant 0.17
rpoC 766799 p.Ala1144Ser missense_variant 0.2
rpoC 766804 c.3435A>G synonymous_variant 0.2
rpoC 766837 c.3468G>C synonymous_variant 0.17
rpoC 766843 c.3474T>G synonymous_variant 0.17
rpoC 767117 p.Glu1250* stop_gained 0.12
rpoC 767145 p.Pro1259Gln missense_variant 0.12
rpoC 767238 c.3870delT frameshift_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777301 p.Leu394Met missense_variant 0.13
mmpR5 779174 p.Ala62Val missense_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781518 c.-42G>T upstream_gene_variant 0.13
rpsL 781633 p.Lys25Arg missense_variant 0.13
fbiC 1305475 p.Thr849Ala missense_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 0.93
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471930 n.85G>A non_coding_transcript_exon_variant 0.5
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.6
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.4
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.5
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.5
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1473122 n.1281delA non_coding_transcript_exon_variant 1.0
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 1.0
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.67
rrs 1473172 n.1327T>G non_coding_transcript_exon_variant 0.6
rrs 1473173 n.1328C>T non_coding_transcript_exon_variant 0.6
rrs 1473221 n.1376C>T non_coding_transcript_exon_variant 0.6
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.5
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.5
rrs 1473276 n.1431A>C non_coding_transcript_exon_variant 0.5
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.5
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.5
rrl 1474164 n.507C>T non_coding_transcript_exon_variant 1.0
rrl 1474181 n.524C>A non_coding_transcript_exon_variant 1.0
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 1.0
rrl 1474197 n.540C>T non_coding_transcript_exon_variant 1.0
rrl 1474199 n.542G>C non_coding_transcript_exon_variant 1.0
rrl 1474200 n.545delT non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1475715 n.2058G>T non_coding_transcript_exon_variant 1.0
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 1.0
rrl 1475755 n.2099_2102delTAAC non_coding_transcript_exon_variant 1.0
rrl 1475761 n.2104C>A non_coding_transcript_exon_variant 1.0
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 1.0
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 1.0
rrl 1475766 n.2109_2110insCTTTTTGTT non_coding_transcript_exon_variant 1.0
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 1.0
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5
rrl 1476492 n.2835G>C non_coding_transcript_exon_variant 1.0
inhA 1673880 c.-322C>T upstream_gene_variant 0.14
rpsA 1833778 c.237C>A synonymous_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834977 p.Gly479Val missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917987 c.48G>T synonymous_variant 0.2
tlyA 1918556 p.Arg206Leu missense_variant 0.2
tlyA 1918565 p.Leu209Pro missense_variant 0.17
katG 2154173 p.Thr647Ala missense_variant 0.25
katG 2154582 c.1530C>A synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168246 c.2367C>A synonymous_variant 0.13
PPE35 2169124 p.Thr497Ala missense_variant 0.29
PPE35 2170066 p.Ala183Thr missense_variant 0.22
Rv1979c 2222198 p.Ala323Ser missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288984 p.Asp86Glu missense_variant 0.1
pncA 2289132 p.Glu37Gly missense_variant 0.17
kasA 2518300 c.186T>C synonymous_variant 0.2
eis 2715049 p.Gly95Asp missense_variant 0.12
ahpC 2726338 p.Val49Gly missense_variant 0.2
folC 2747469 p.Asp44Asn missense_variant 0.15
ribD 2986765 c.-74G>T upstream_gene_variant 0.11
ribD 2987007 p.Gly57Cys missense_variant 0.29
ribD 2987185 p.Gln116Arg missense_variant 0.12
ribD 2987598 p.Arg254Ser missense_variant 0.11
Rv2752c 3064518 c.1674G>T synonymous_variant 0.1
Rv2752c 3065071 p.Gly374Val missense_variant 0.11
Rv2752c 3065737 p.Asp152Gly missense_variant 0.13
ald 3086781 c.-39T>C upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087478 p.Ser220* stop_gained 0.11
ald 3087608 c.789A>G synonymous_variant 0.12
ald 3087675 p.Pro286Thr missense_variant 0.12
Rv3083 3448640 p.Asp46Val missense_variant 0.14
Rv3083 3449272 p.Ala257Thr missense_variant 0.13
Rv3083 3449360 c.858delC frameshift_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474237 c.231C>T synonymous_variant 0.17
fprA 3474997 p.Gly331Trp missense_variant 0.25
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640861 p.Arg107Cys missense_variant 0.12
alr 3840607 p.Val272Met missense_variant 0.14
alr 3841141 p.Val94Ile missense_variant 0.12
rpoA 3877482 c.1026C>A synonymous_variant 0.15
rpoA 3878683 c.-176G>C upstream_gene_variant 0.2
embC 4240045 p.Trp61Cys missense_variant 0.22
embC 4240585 c.723C>T synonymous_variant 0.12
embC 4240646 p.Phe262Leu missense_variant 0.15
embC 4241296 c.1434C>G synonymous_variant 0.1
embC 4241524 p.Lys554Asn missense_variant 0.12
embC 4241945 p.Arg695Trp missense_variant 0.12
embC 4242104 p.Thr748Ala missense_variant 0.11
embC 4242617 p.Asp919Asn missense_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245491 c.2261delC frameshift_variant 0.17
embB 4246307 c.-207G>T upstream_gene_variant 0.17
embB 4246797 p.Gly95Ala missense_variant 0.22
embB 4248536 p.Leu675Met missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4268929 p.Gly302Asp missense_variant 0.11
ethA 4327472 c.2T>C start_lost 1.0
ethA 4327528 c.-55C>A upstream_gene_variant 0.15
whiB6 4338233 p.Ser97Pro missense_variant 1.0
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