TB-Profiler result

Run: SRR18002991
Summary

Run ID: SRR18002991

Sample name:

Date: 03-04-2023 19:12:53

Number of reads: 3361781

Percentage reads mapped: 86.38

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761140 p.His445Arg missense_variant 1.0 rifampicin
pncA 2288835 p.Asp136Gly missense_variant 1.0 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 0.96 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326648 c.825delG frameshift_variant 0.99 ethionamide, ethionamide
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 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.26
mshA 576413 p.Gly356Ser missense_variant 0.29
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 762779 c.-591C>T upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765065 p.Leu566Val missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.33
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>C non_coding_transcript_exon_variant 0.29
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.15
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.15
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.15
rrs 1473097 n.1252G>A non_coding_transcript_exon_variant 0.12
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.12
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.12
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.12
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.11
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.11
rrs 1473134 n.1289T>C non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473147 n.1302G>A non_coding_transcript_exon_variant 0.14
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrl 1474454 n.797G>A non_coding_transcript_exon_variant 0.33
rrl 1474466 n.809G>A non_coding_transcript_exon_variant 0.4
rrl 1474476 n.819C>G non_coding_transcript_exon_variant 0.4
rrl 1474483 n.826C>G non_coding_transcript_exon_variant 0.4
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.4
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.4
rrl 1474527 n.870T>C non_coding_transcript_exon_variant 0.5
rrl 1474528 n.871T>A non_coding_transcript_exon_variant 0.5
rrl 1474529 n.872A>G non_coding_transcript_exon_variant 0.5
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.33
rrl 1474540 n.883T>C non_coding_transcript_exon_variant 0.33
rrl 1474541 n.884G>T non_coding_transcript_exon_variant 0.33
rrl 1474542 n.885A>G non_coding_transcript_exon_variant 0.33
rrl 1474551 n.894G>C non_coding_transcript_exon_variant 0.43
rrl 1474558 n.901G>T non_coding_transcript_exon_variant 0.43
rrl 1474583 n.926C>T non_coding_transcript_exon_variant 0.57
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.33
rrl 1474627 n.970G>A non_coding_transcript_exon_variant 0.33
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.33
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.4
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.4
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.4
rrl 1474639 n.982G>C non_coding_transcript_exon_variant 0.4
rrl 1474676 n.1019T>A non_coding_transcript_exon_variant 0.4
rrl 1475579 n.1922G>T non_coding_transcript_exon_variant 0.2
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.18
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.4
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.4
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.4
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.4
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.4
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.4
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.2
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.22
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.2
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.36
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.36
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.45
rrl 1476368 n.2711T>C non_coding_transcript_exon_variant 0.36
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.45
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.42
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.45
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.38
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.38
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.45
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.55
rrl 1476470 n.2813C>T non_coding_transcript_exon_variant 0.36
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.45
rrl 1476491 n.2834T>C non_coding_transcript_exon_variant 0.33
rrl 1476501 n.2844C>T non_coding_transcript_exon_variant 0.2
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.3
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.2
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.3
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.27
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.17
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.18
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918582 p.Ala215Pro missense_variant 0.97
ndh 2101845 p.His400Tyr missense_variant 0.31
ndh 2102361 c.681dupG frameshift_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154800 p.Trp438Arg missense_variant 0.98
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223010 p.Val52Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embB 4247028 p.Leu172Arg missense_variant 0.28
aftB 4267647 p.Asp397Gly 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