TB-Profiler result

Run: SRR1002680
Summary

Run ID: SRR1002680

Sample name:

Date: 02-04-2023 14:19:34

Number of reads: 1080776

Percentage reads mapped: 97.89

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 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288730 p.Ala171Val missense_variant 1.0 pyrazinamide
pncA 2288957 p.Tyr95* stop_gained 0.15 pyrazinamide
eis 2715342 c.-10G>A upstream_gene_variant 1.0 kanamycin
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326770 c.703delT frameshift_variant 1.0 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 575848 p.Asp167Glu missense_variant 0.13
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760087 p.Ser94Phe missense_variant 0.25
rpoB 760342 p.Val179Gly missense_variant 0.2
rpoB 762364 p.Asp853Gly missense_variant 0.2
rpoC 762377 c.-993C>A upstream_gene_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763645 p.Met92Ile missense_variant 0.17
rpoC 764633 p.Val422Ile missense_variant 0.14
rpoC 764828 p.Leu487Phe missense_variant 0.2
rpoC 765463 p.Asn698Lys missense_variant 1.0
rpoC 766158 p.Val930Gly missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775825 c.2656C>T synonymous_variant 0.17
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777164 c.1317C>T synonymous_variant 0.25
mmpL5 777173 c.1308C>T synonymous_variant 0.25
mmpL5 777176 p.Glu435Asp missense_variant 0.25
mmpL5 777492 p.Pro330Gln missense_variant 0.17
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304020 p.His364Tyr missense_variant 0.5
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416222 p.Phe376Leu missense_variant 0.18
embR 1416232 p.Cys372Gly missense_variant 0.13
embR 1416259 c.1089G>C synonymous_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472647 n.802C>T non_coding_transcript_exon_variant 0.33
rrl 1473674 n.17G>A non_coding_transcript_exon_variant 0.25
rrl 1474041 n.386delG non_coding_transcript_exon_variant 0.25
rrl 1475075 n.1418A>C non_coding_transcript_exon_variant 0.4
rrl 1475555 n.1898T>G non_coding_transcript_exon_variant 0.15
rrl 1475586 n.1929C>T non_coding_transcript_exon_variant 0.17
rrl 1475591 n.1934G>T non_coding_transcript_exon_variant 0.17
rrl 1475637 n.1980T>A non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.18
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.33
fabG1 1673380 c.-60C>G upstream_gene_variant 0.5
rpsA 1833420 c.-122C>T upstream_gene_variant 0.13
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918263 c.324G>C synonymous_variant 0.25
ndh 2102417 p.Ala209Val missense_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167879 p.Ser912Gly missense_variant 0.17
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169488 c.1125G>C synonymous_variant 0.2
PPE35 2169491 c.1122T>C synonymous_variant 0.2
PPE35 2169602 c.1011C>A synonymous_variant 0.17
PPE35 2170517 c.96C>T synonymous_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746923 p.Gly226Ser missense_variant 0.5
ribD 2987059 p.Leu74Ser missense_variant 0.22
Rv2752c 3066067 p.Ile42Thr missense_variant 0.2
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087876 p.Glu353Lys missense_variant 0.15
Rv3083 3448641 c.138C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568776 c.-97G>T upstream_gene_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.14
alr 3841612 c.-193_-192insC upstream_gene_variant 0.27
ddn 3986926 p.Met28Thr missense_variant 0.22
clpC1 4040309 c.396C>T synonymous_variant 0.12
clpC1 4040682 p.Arg8Leu missense_variant 0.25
embC 4240124 p.Cys88Arg missense_variant 0.33
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243187 c.-46C>G upstream_gene_variant 0.17
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243580 c.348G>A synonymous_variant 0.22
embA 4244656 p.Thr475Lys missense_variant 0.25
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246555 c.42G>C synonymous_variant 0.25
embB 4246556 p.Ala15Pro missense_variant 0.25
embB 4246567 c.54_55insT frameshift_variant 0.2
embB 4247286 p.Pro258His missense_variant 0.14
embB 4248692 p.Val727Leu missense_variant 0.33
aftB 4267422 p.Thr472Ile missense_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269638 p.Ala66Thr missense_variant 0.5
ubiA 4269640 p.Ala65Asp missense_variant 0.5
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338403 p.Arg40His missense_variant 0.29
whiB6 4338499 p.Glu8Gly missense_variant 0.33
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