TB-Profiler result

Run: ERR4831745
Summary

Run ID: ERR4831745

Sample name:

Date: 01-04-2023 21:05:47

Number of reads: 1887064

Percentage reads mapped: 96.22

Strain: lineage2.2.1.1

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
lineage2 East-Asian Beijing RD105 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
lineage2.2.1.1 East-Asian (Beijing) Beijing-RD150 RD105;RD207;RD181;RD150 0.98
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 761140 p.His445Pro missense_variant 0.8 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.13 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288751 p.Ser164* stop_gained 1.0 pyrazinamide
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 6824 c.-478C>T upstream_gene_variant 0.12
gyrA 6841 c.-461T>C upstream_gene_variant 0.1
gyrA 6889 c.-413G>A upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8784 p.Arg495Ser missense_variant 0.17
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575580 c.235delC frameshift_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576302 p.Leu319Met missense_variant 0.14
ccsA 620010 c.120C>A synonymous_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759615 c.-192A>C upstream_gene_variant 0.23
rpoB 760541 c.735G>C synonymous_variant 0.12
rpoB 760561 c.757_758delCG frameshift_variant 0.13
rpoB 760567 p.Ser254Trp missense_variant 0.11
rpoB 762233 c.2427G>C synonymous_variant 0.14
rpoB 762245 c.2439G>C synonymous_variant 0.17
rpoC 762728 c.-642C>G upstream_gene_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763088 c.-282C>G upstream_gene_variant 0.12
rpoC 763094 c.-276G>C upstream_gene_variant 0.11
rpoC 764331 p.Pro321Gln missense_variant 0.12
rpoC 764542 c.1173C>T synonymous_variant 0.13
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 777776 p.Met235Ile missense_variant 0.11
mmpL5 777841 p.Val214Leu missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 0.94
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303144 p.Ser72Pro missense_variant 0.12
fbiC 1303155 c.225G>A synonymous_variant 0.11
fbiC 1304000 p.Val357Ala missense_variant 0.1
fbiC 1304451 c.1521C>T synonymous_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407005 c.336G>C synonymous_variant 0.13
Rv1258c 1407179 c.162G>T synonymous_variant 0.14
Rv1258c 1407399 c.-59C>T upstream_gene_variant 0.33
embR 1416523 c.825G>T synonymous_variant 0.15
embR 1416534 p.Gly272Ser missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472162 n.317G>T non_coding_transcript_exon_variant 0.17
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.14
rrs 1472712 n.867G>T non_coding_transcript_exon_variant 0.12
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.13
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.13
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.25
rrl 1474980 n.1323G>T non_coding_transcript_exon_variant 0.18
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.18
rrl 1475136 n.1479G>A non_coding_transcript_exon_variant 0.14
rrl 1475337 n.1680C>T non_coding_transcript_exon_variant 0.12
rrl 1475343 n.1686A>G non_coding_transcript_exon_variant 0.12
rrl 1475346 n.1689C>T non_coding_transcript_exon_variant 0.13
rrl 1475353 n.1696A>T non_coding_transcript_exon_variant 0.17
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.12
rrl 1475358 n.1701T>C non_coding_transcript_exon_variant 0.12
rrl 1475361 n.1704G>A non_coding_transcript_exon_variant 0.11
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.12
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.12
rrl 1476504 n.2847T>C non_coding_transcript_exon_variant 0.11
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.11
rpsA 1833353 c.-189C>T upstream_gene_variant 0.12
rpsA 1833838 c.297G>C synonymous_variant 0.1
rpsA 1834177 c.636A>C synonymous_variant 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918572 c.633C>A synonymous_variant 0.18
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170028 p.Met195Ile missense_variant 0.11
PPE35 2170123 p.Ala164Ser missense_variant 0.14
PPE35 2170292 c.321G>C synonymous_variant 0.1
PPE35 2170395 p.Ala73Val missense_variant 0.22
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518905 p.Arg264Gln missense_variant 0.15
kasA 2518918 c.804C>G synonymous_variant 0.12
kasA 2519032 c.918C>T synonymous_variant 0.17
kasA 2519202 p.Arg363Leu missense_variant 0.12
eis 2714846 p.Val163Ile missense_variant 1.0
ahpC 2726350 p.Trp53Leu missense_variant 0.21
folC 2746244 p.Ala452Asp missense_variant 0.12
folC 2746309 c.1290G>T synonymous_variant 0.25
folC 2746588 c.1011C>T synonymous_variant 0.14
folC 2746883 p.Pro239Gln missense_variant 0.14
folC 2747053 c.546C>T synonymous_variant 0.2
folC 2747631 c.-33C>A upstream_gene_variant 0.12
Rv2752c 3065669 p.Gln175Lys missense_variant 0.11
Rv2752c 3067155 c.-964C>T upstream_gene_variant 0.17
thyX 3067388 c.558C>T synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449142 c.639C>A synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612161 p.Ala319Gly missense_variant 0.12
Rv3236c 3612813 p.Thr102Ala missense_variant 0.94
fbiA 3640407 c.-136G>A upstream_gene_variant 1.0
fbiB 3642197 c.663C>G synonymous_variant 0.2
alr 3840498 p.Ala308Glu missense_variant 0.12
rpoA 3878637 c.-130G>A upstream_gene_variant 1.0
clpC1 4039032 p.Gly558Asp missense_variant 0.22
clpC1 4039096 p.Ala537Ser missense_variant 0.14
clpC1 4040078 p.Lys209Asn missense_variant 0.14
embC 4240671 p.Thr270Ile missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243488 p.Gly86Ser missense_variant 0.12
embA 4244899 p.Thr556Met missense_variant 0.13
embA 4245597 p.Lys789Glu missense_variant 0.13
embA 4246009 p.Arg926Gln missense_variant 0.15
embA 4246018 p.Leu929Pro missense_variant 0.15
embB 4246861 c.348C>A synonymous_variant 0.15
embB 4246977 p.Ala155Val missense_variant 0.17
embB 4248115 c.1602C>T synonymous_variant 1.0
embB 4249286 p.Gln925Lys missense_variant 0.14
embB 4249475 p.Trp988Arg missense_variant 0.12
embB 4249650 p.Ala1046Val missense_variant 0.12
embB 4249753 p.Leu1080Phe missense_variant 0.11
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4328043 c.-570G>T upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.94
gid 4407927 p.Glu92Asp missense_variant 1.0