TB-Profiler result

Run: ERR036198
Summary

Run ID: ERR036198

Sample name:

Date: 31-03-2023 08:29:11

Number of reads: 926889

Percentage reads mapped: 95.97

Strain: lineage4.3.4.2

Drug-resistance: Other

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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 0.73
lineage4.3 Euro-American (LAM) mainly-LAM None 0.61
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.11
lineage4.3.4 Euro-American (LAM) LAM RD174 0.6
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 0.53
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 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
gid 4407816 c.386delG frameshift_variant 0.12 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
gyrB 6112 p.Met291Ile missense_variant 0.17
gyrB 6140 p.Val301Leu missense_variant 0.57
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.75
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8056 p.Arg252Leu missense_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 0.82
fgd1 491014 p.Thr78Pro missense_variant 0.33
fgd1 491315 p.Gly178Ala missense_variant 0.43
fgd1 491742 c.960T>C synonymous_variant 0.14
rpoB 759746 c.-61C>T upstream_gene_variant 0.18
rpoB 759831 p.Thr9Pro missense_variant 0.42
rpoB 762249 p.Leu815Val missense_variant 0.33
rpoC 762434 c.-936T>G upstream_gene_variant 0.14
rpoC 762836 c.-534C>G upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 0.29
rpoC 764725 p.Phe452Leu missense_variant 0.27
rpoC 764995 c.1626C>G synonymous_variant 0.71
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776038 c.2442delC frameshift_variant 0.15
mmpL5 776100 p.Thr794Ile missense_variant 0.22
mmpL5 777399 p.Thr361Arg missense_variant 0.31
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800997 p.Asn63Lys missense_variant 0.18
rplC 801166 p.Gly120Ser missense_variant 0.12
Rv1258c 1406750 c.591C>A synonymous_variant 0.2
embR 1417501 c.-154A>C upstream_gene_variant 0.28
atpE 1461019 c.-26C>A upstream_gene_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.23
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.14
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.21
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.2
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.12
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.12
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.29
rrs 1473369 n.1524A>G non_coding_transcript_exon_variant 0.2
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.22
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 0.12
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.5
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.16
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.14
rrl 1474601 n.944C>T non_coding_transcript_exon_variant 0.13
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.25
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.12
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.12
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.12
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.12
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.13
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.12
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.1
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.15
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.18
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.17
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.17
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.15
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
inhA 1674892 p.Asn231Asp missense_variant 0.3
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101850 p.Val398Gly missense_variant 0.33
ndh 2102540 p.Ala168Gly missense_variant 0.22
katG 2154532 p.Ser527Leu missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.3
PPE35 2167926 p.Leu896Ser missense_variant 0.33
PPE35 2167983 p.Gly877Asp missense_variant 0.23
PPE35 2169866 c.747G>C synonymous_variant 0.36
Rv1979c 2222308 p.Asp286Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289365 c.-125delC upstream_gene_variant 0.15
eis 2714569 p.Ala255Gly missense_variant 0.25
eis 2715586 c.-254G>C upstream_gene_variant 0.67
ahpC 2726051 c.-142G>A upstream_gene_variant 0.2
ahpC 2726105 c.-88G>A upstream_gene_variant 0.18
folC 2747263 c.336C>A synonymous_variant 0.25
Rv2752c 3064552 p.Arg547Pro missense_variant 0.62
Rv2752c 3064741 p.Gly484Ala missense_variant 0.45
thyX 3067995 c.-50A>C upstream_gene_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 0.82
ald 3086788 c.-32T>C upstream_gene_variant 0.89
fbiD 3339153 p.Leu12Phe missense_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.92
Rv3236c 3612009 p.Ala370Thr missense_variant 0.62
alr 3840268 p.Thr385Pro missense_variant 0.29
alr 3840719 c.702A>G synonymous_variant 0.5
rpoA 3878238 p.Asp90Glu missense_variant 0.2
rpoA 3878687 c.-180A>C upstream_gene_variant 0.18
ddn 3987013 p.Gly57Ala missense_variant 0.31
clpC1 4038287 c.2418C>T synonymous_variant 0.67
clpC1 4039363 p.Ala448Pro missense_variant 0.35
clpC1 4040517 p.Val63Ala missense_variant 0.12
embC 4240646 p.Phe262Val missense_variant 0.29
embC 4242075 p.Arg738Gln missense_variant 0.17
embC 4242425 p.Arg855Gly missense_variant 0.2
embC 4242476 p.Pro872Ala missense_variant 0.27
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.46
embC 4242827 p.Leu989Val missense_variant 0.33
embA 4243848 p.Val206Met missense_variant 0.12
embA 4245969 p.Pro913Ser missense_variant 0.24
embB 4247126 p.Thr205Ala missense_variant 0.12
ubiA 4269387 p.Glu149Asp missense_variant 0.17
ubiA 4269529 p.Ala102Gly missense_variant 0.33
aftB 4269606 c.-770T>C upstream_gene_variant 0.12
ubiA 4269920 c.-87G>A upstream_gene_variant 0.25
ethA 4328212 c.-740delC upstream_gene_variant 0.15
whiB6 4338371 p.Thr51Pro missense_variant 0.12
whiB6 4338493 p.Thr10Lys missense_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 0.23
gid 4407780 c.423G>A synonymous_variant 0.23
gid 4408156 p.Leu16Arg missense_variant 0.68