TB-Profiler result

Run: ERR2229435
Summary

Run ID: ERR2229435

Sample name:

Date: 31-03-2023 17:11:07

Number of reads: 447760

Percentage reads mapped: 97.96

Strain: lineage4.8

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 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.29 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473329 n.1484G>T non_coding_transcript_exon_variant 0.14 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155247 c.864dupC frameshift_variant 0.25 isoniazid
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 7714 p.Ala138Val missense_variant 0.14
fgd1 491055 c.273C>T synonymous_variant 0.12
fgd1 491648 c.870delC frameshift_variant 0.14
rpoC 765829 p.Met820Ile missense_variant 0.25
rpoC 766568 c.3201delT frameshift_variant 0.2
rpoC 766836 p.Val1156Glu missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303508 p.Pro193Gln missense_variant 0.25
fbiC 1303747 p.Thr273Ala missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472421 n.576G>A non_coding_transcript_exon_variant 0.11
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.22
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.29
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.14
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.15
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.23
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.23
rrs 1473288 n.1443C>G non_coding_transcript_exon_variant 0.17
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.17
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.17
rrs 1473294 n.1449A>G non_coding_transcript_exon_variant 0.17
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.17
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.14
rrs 1473319 n.1474C>T non_coding_transcript_exon_variant 0.14
rrs 1473324 n.1479G>A non_coding_transcript_exon_variant 0.14
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.3
rrl 1474752 n.1096delA non_coding_transcript_exon_variant 0.3
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.4
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.25
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.25
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.25
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.33
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.33
rrl 1474799 n.1143delT non_coding_transcript_exon_variant 0.33
rrl 1474803 n.1146_1147insA non_coding_transcript_exon_variant 0.33
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.33
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.36
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.27
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.27
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.27
rrl 1474853 n.1196A>G non_coding_transcript_exon_variant 0.31
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.33
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.33
rrl 1475385 n.1728G>A non_coding_transcript_exon_variant 0.13
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.23
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.23
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.23
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.21
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.23
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.25
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.25
rrl 1475892 n.2235A>C non_coding_transcript_exon_variant 0.27
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.23
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.23
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.27
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.27
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.3
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.18
rrl 1476206 n.2550delT non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.25
rrl 1476363 n.2706A>G non_coding_transcript_exon_variant 0.29
rrl 1476366 n.2709A>C non_coding_transcript_exon_variant 0.29
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.25
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.25
rrl 1476374 n.2717T>G non_coding_transcript_exon_variant 0.29
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
fabG1 1673560 p.Lys41Leu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102071 c.972C>T synonymous_variant 0.25
katG 2154807 c.1305C>G synonymous_variant 0.18
katG 2156478 c.-367A>T upstream_gene_variant 0.12
PPE35 2167965 p.Ala883Gly missense_variant 0.5
PPE35 2167967 c.2646A>C synonymous_variant 0.5
PPE35 2168637 p.Pro659Leu missense_variant 0.12
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2169302 p.Met437Ile missense_variant 0.11
PPE35 2169884 c.729T>C synonymous_variant 0.13
PPE35 2169902 p.Leu237Phe missense_variant 0.29
PPE35 2169910 p.Asn235Tyr missense_variant 0.31
PPE35 2170048 p.Leu189Val missense_variant 0.18
PPE35 2170053 p.Thr187Ser missense_variant 0.2
PPE35 2170189 p.Glu142Gln missense_variant 0.21
PPE35 2170190 c.423G>A synonymous_variant 0.14
PPE35 2170387 c.226C>T synonymous_variant 0.18
Rv1979c 2222962 p.Ala68Gly missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290189 c.-948G>T upstream_gene_variant 0.4
eis 2714661 c.672G>T synonymous_variant 0.2
eis 2715061 p.His91Arg missense_variant 0.13
folC 2746809 p.Ala264Thr missense_variant 0.33
pepQ 2859375 c.1044G>A synonymous_variant 0.13
ribD 2987265 p.Leu143Ile missense_variant 0.12
Rv2752c 3065152 p.Ala347Val missense_variant 0.2
Rv2752c 3066277 c.-86C>T upstream_gene_variant 0.2
fbiD 3339749 p.Val211Gly missense_variant 0.25
fbiB 3641813 p.Leu93Phe missense_variant 0.22
fbiB 3642149 c.615C>A synonymous_variant 0.17
ddn 3987088 p.Ala82Glu missense_variant 0.12
clpC1 4038501 p.Ile735Thr missense_variant 1.0
clpC1 4038786 p.Gln640Pro missense_variant 0.13
clpC1 4039161 p.His515Gly missense_variant 0.13
clpC1 4039169 p.Glu512Asp missense_variant 0.13
clpC1 4040026 p.Glu227Lys missense_variant 0.33
embC 4242519 p.Thr886Met missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242759 p.Pro966Gln missense_variant 0.33
embA 4244821 p.Gly530Val missense_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.2
aftB 4268193 p.Leu215Pro missense_variant 0.18
ubiA 4269842 c.-9T>C upstream_gene_variant 0.22
ethR 4326961 c.-588G>C upstream_gene_variant 0.12
ethR 4326964 c.-585G>A upstream_gene_variant 0.13
ethR 4326970 c.-579G>T upstream_gene_variant 0.18
ethR 4326982 c.-567C>G upstream_gene_variant 0.12
ethA 4327256 p.Gln73Arg missense_variant 0.18
ethA 4327527 c.-54G>T upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408346 c.-144G>T upstream_gene_variant 0.13
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0