TB-Profiler result

Run: SRR7645929
Summary

Run ID: SRR7645929

Sample name:

Date: 04-04-2023 19:59:07

Number of reads: 683720

Percentage reads mapped: 95.43

Strain: lineage2.2.1

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 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 1.0 pyrazinamide
thyX 3067961 c.-16C>T upstream_gene_variant 1.0 para-aminosalicylic_acid
thyA 3073808 p.Arg222Gly missense_variant 1.0 para-aminosalicylic_acid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
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 6525 p.Arg429His missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8952 p.Gln551* stop_gained 0.12
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 576357 p.Ala337Val missense_variant 0.14
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620681 p.Lys264Thr missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763041 p.Leu1079Met missense_variant 0.12
rpoC 763546 c.177A>G synonymous_variant 0.12
rpoC 763551 p.Tyr61Ser missense_variant 0.13
rpoC 763570 c.201G>C synonymous_variant 0.18
rpoC 763578 p.Phe70Tyr missense_variant 0.2
rpoC 766333 c.2964G>T synonymous_variant 0.15
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766779 p.Glu1137Gly 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 1.0
mmpR5 779291 p.Ala101Val missense_variant 0.2
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781478 c.-82C>T upstream_gene_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
atpE 1461059 c.15C>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.18
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.21
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.18
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.16
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.23
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.28
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.27
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.26
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.14
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.14
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.21
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.16
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.16
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.19
rrs 1473164 n.1319C>T non_coding_transcript_exon_variant 0.1
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.11
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.16
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.17
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.17
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.17
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.16
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.16
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.21
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.16
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.16
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.15
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.19
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.19
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.12
rrl 1476091 n.2434T>C non_coding_transcript_exon_variant 1.0
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.12
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.21
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.2
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.2
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.21
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.21
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.21
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.21
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.15
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.11
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.14
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.18
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834612 c.1071G>T synonymous_variant 0.25
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101839 p.Ala402Thr missense_variant 0.13
katG 2154259 p.Thr618Met missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518642 c.528A>G synonymous_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087494 c.675C>A synonymous_variant 0.12
Rv3083 3448583 c.84delC frameshift_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641810 c.276G>C synonymous_variant 1.0
alr 3840576 p.Ala282Val missense_variant 0.16
rpoA 3877773 c.735G>A synonymous_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.17
ethA 4326339 p.Asn379Asp 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