TB-Profiler result

Run: ERR4831841
Summary

Run ID: ERR4831841

Sample name:

Date: 01-04-2023 21:09:33

Number of reads: 1690482

Percentage reads mapped: 92.8

Strain: lineage4.4.2;lineage2.2.1

Drug-resistance: HR-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 0.91
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.08
lineage4.4 Euro-American S;T None 0.91
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.05
lineage4.4.2 Euro-American T1;T2 None 0.9
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
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
gid 4408100 c.102delG frameshift_variant 0.98 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 7168 c.-134C>G upstream_gene_variant 0.11
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491424 c.642C>T synonymous_variant 0.12
fgd1 491454 c.672C>A synonymous_variant 0.13
rpoB 760181 c.375T>C synonymous_variant 0.12
rpoB 760184 c.378A>G synonymous_variant 0.11
rpoB 760193 c.387C>G synonymous_variant 0.12
rpoB 760196 c.390C>G synonymous_variant 0.12
rpoB 760235 c.429T>C synonymous_variant 0.12
rpoB 760244 c.438G>C synonymous_variant 0.1
rpoB 761147 c.1341C>T synonymous_variant 0.13
rpoB 761150 c.1344A>T synonymous_variant 0.12
rpoB 761165 c.1359G>C synonymous_variant 0.12
rpoB 761171 c.1365C>T synonymous_variant 0.12
rpoB 761180 c.1374A>C synonymous_variant 0.11
rpoB 761186 p.Glu460Asp missense_variant 0.11
rpoB 761189 c.1383T>C synonymous_variant 0.11
rpoB 761195 c.1389G>C synonymous_variant 0.11
rpoB 761198 c.1392G>C synonymous_variant 0.11
rpoB 762101 c.2295C>G synonymous_variant 0.11
rpoB 762114 p.Ile770Val missense_variant 0.1
rpoB 762194 c.2388G>C synonymous_variant 0.1
rpoC 762917 c.-453C>G upstream_gene_variant 0.12
rpoC 762920 c.-450C>T upstream_gene_variant 0.2
rpoC 762923 c.-447C>G upstream_gene_variant 0.19
rpoC 762929 c.-441G>C upstream_gene_variant 0.22
rpoC 762959 c.-411G>C upstream_gene_variant 0.28
rpoC 762962 c.-408C>T upstream_gene_variant 0.24
rpoC 763031 c.-339T>C upstream_gene_variant 0.35
rpoC 763915 c.546C>T synonymous_variant 0.87
rpoC 763933 c.564C>T synonymous_variant 0.11
rpoC 763940 p.Ala191Ser missense_variant 0.14
rpoC 764824 c.1455T>C synonymous_variant 0.12
rpoC 764827 c.1458G>C synonymous_variant 0.12
rpoC 764858 c.1489T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779054 p.Gln22Arg missense_variant 0.89
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303047 c.117G>A synonymous_variant 0.93
embR 1416989 c.358delA frameshift_variant 0.97
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.14
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.14
rrs 1472848 n.1003T>C non_coding_transcript_exon_variant 0.11
rrs 1472861 n.1016G>A non_coding_transcript_exon_variant 0.12
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.24
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.21
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.14
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.14
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.14
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.15
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.15
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14
rrs 1473082 n.1237G>A non_coding_transcript_exon_variant 0.25
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.15
rrl 1473953 n.296T>C non_coding_transcript_exon_variant 0.13
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.27
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.25
rrl 1474387 n.730C>T non_coding_transcript_exon_variant 0.13
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.17
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.17
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.2
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.2
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.15
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.11
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.17
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.16
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.15
rrl 1475475 n.1818C>T non_coding_transcript_exon_variant 0.14
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.12
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.12
rrl 1475488 n.1831G>T non_coding_transcript_exon_variant 0.12
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.2
rrl 1475602 n.1945G>T non_coding_transcript_exon_variant 0.12
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.13
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.13
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.12
rrl 1475989 n.2332T>C non_coding_transcript_exon_variant 0.12
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.12
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.18
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.13
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.12
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.11
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.2
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.28
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.27
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.27
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.27
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.25
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14
rpsA 1833619 c.78A>C synonymous_variant 0.12
rpsA 1833625 c.84A>G synonymous_variant 0.12
rpsA 1833664 c.123C>G synonymous_variant 0.11
rpsA 1833676 c.135A>G synonymous_variant 0.12
rpsA 1833679 c.138G>T synonymous_variant 0.11
rpsA 1833685 c.144G>C synonymous_variant 0.11
rpsA 1833691 c.150G>A synonymous_variant 0.12
rpsA 1833694 c.153G>T synonymous_variant 0.12
rpsA 1833697 c.156C>T synonymous_variant 0.12
rpsA 1833700 c.159C>T synonymous_variant 0.12
rpsA 1833709 c.168C>T synonymous_variant 0.11
rpsA 1833760 c.219C>T synonymous_variant 0.17
rpsA 1833787 c.246C>G synonymous_variant 0.11
rpsA 1833790 c.249T>C synonymous_variant 0.11
rpsA 1834177 c.636A>C synonymous_variant 0.11
rpsA 1834261 c.720A>G synonymous_variant 0.11
rpsA 1834264 c.723G>C synonymous_variant 0.11
rpsA 1834357 c.816T>C synonymous_variant 0.13
rpsA 1834366 c.825A>G synonymous_variant 0.13
rpsA 1834375 c.834G>C synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 0.2
PPE35 2170048 p.Leu189Val missense_variant 0.25
PPE35 2170053 p.Thr187Ser missense_variant 0.25
Rv1979c 2221889 p.Val426Ile missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2517917 c.-198G>C upstream_gene_variant 0.13
Rv2752c 3066099 p.Met31Ile missense_variant 0.83
ald 3086742 c.-78A>C upstream_gene_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.89
Rv3083 3448714 p.Asp71His missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 0.25
clpC1 4038612 p.Asn698Ser missense_variant 0.98
clpC1 4039022 c.1683A>G synonymous_variant 0.15
embC 4240671 p.Thr270Ile missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.83
embB 4247249 p.Gly246Arg missense_variant 0.94
aftB 4267647 p.Asp397Gly missense_variant 0.12
aftB 4268928 c.-92C>T upstream_gene_variant 0.81
aftB 4269375 c.-539G>A upstream_gene_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 0.14