TB-Profiler result

Run: ERR1577244
Summary

Run ID: ERR1577244

Sample name:

Date: 31-03-2023 14:38:38

Number of reads: 846061

Percentage reads mapped: 99.16

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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
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 5813 p.Arg192Gly missense_variant 0.12
gyrB 6023 p.Lys262Glu missense_variant 0.17
gyrB 6874 p.Leu545Phe missense_variant 0.19
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7826 c.525C>G synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490819 p.Glu13Gln missense_variant 0.12
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575253 c.-95G>A upstream_gene_variant 0.14
mshA 575320 c.-27delG upstream_gene_variant 0.12
mshA 575436 p.Pro30Gln missense_variant 0.14
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576094 c.747G>T synonymous_variant 0.17
mshA 576380 p.Leu345Met missense_variant 0.18
mshA 576383 p.Val346Phe missense_variant 0.18
mshA 576423 p.Ala359Asp missense_variant 0.17
mshA 576773 p.Arg476Gly missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620641 p.Ala251Thr missense_variant 0.22
ccsA 620859 c.969G>A synonymous_variant 1.0
rpoB 759806 c.-1C>A upstream_gene_variant 0.15
rpoB 760499 c.693G>T synonymous_variant 0.15
rpoB 762578 p.Gln924His missense_variant 0.18
rpoB 762627 p.Asp941Tyr missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763052 c.-318G>T upstream_gene_variant 0.2
rpoC 763088 c.-282C>G upstream_gene_variant 0.15
rpoC 763926 p.Ala186Gly missense_variant 0.11
rpoC 765060 p.Asn564Ser missense_variant 1.0
rpoC 765170 p.Pro601Ala missense_variant 0.11
rpoC 766364 p.Ala999Ser missense_variant 0.14
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766882 c.3513C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776263 p.Thr740Pro missense_variant 0.11
mmpL5 777270 p.Gly404Ala missense_variant 0.13
mmpL5 777292 p.Ala397Ser missense_variant 0.15
mmpS5 778884 p.Ala8Thr missense_variant 0.15
mmpR5 779119 p.Leu44Met missense_variant 0.14
mmpR5 779240 p.Ala84Val missense_variant 0.15
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800892 c.84G>C synonymous_variant 0.11
fbiC 1303106 p.Cys59Phe missense_variant 0.15
fbiC 1304502 c.1572G>T synonymous_variant 0.18
fbiC 1304527 p.Asp533His missense_variant 0.13
fbiC 1304628 c.1698G>T synonymous_variant 0.15
fbiC 1305493 p.Ala855Ser missense_variant 0.15
Rv1258c 1406729 c.612G>C synonymous_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406846 c.495C>A synonymous_variant 0.17
Rv1258c 1406957 c.384G>C synonymous_variant 0.17
Rv1258c 1407153 p.Gly63Asp missense_variant 0.15
embR 1417111 p.Leu79Ile missense_variant 0.13
embR 1417123 p.Tyr75* stop_gained 0.15
embR 1417154 p.Pro65Leu missense_variant 0.15
embR 1417162 c.185delA frameshift_variant 0.17
atpE 1461166 p.Arg41Pro missense_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472181 n.336G>T non_coding_transcript_exon_variant 0.33
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.2
rrs 1472719 n.874G>T non_coding_transcript_exon_variant 0.18
rrs 1472734 n.889C>A non_coding_transcript_exon_variant 0.17
rrs 1472783 n.938G>T non_coding_transcript_exon_variant 0.22
rrs 1472804 n.959G>T non_coding_transcript_exon_variant 0.2
rrs 1472825 n.980G>T non_coding_transcript_exon_variant 0.15
rrs 1472924 n.1079G>T non_coding_transcript_exon_variant 0.2
rrs 1472981 n.1136G>T non_coding_transcript_exon_variant 0.22
rrs 1473245 n.1400C>T non_coding_transcript_exon_variant 0.15
rrl 1473483 n.-175C>A upstream_gene_variant 0.14
rrl 1473809 n.152C>A non_coding_transcript_exon_variant 0.33
rrl 1473991 n.334C>A non_coding_transcript_exon_variant 0.18
rrl 1474008 n.351G>C non_coding_transcript_exon_variant 0.17
rrl 1474260 n.603A>G non_coding_transcript_exon_variant 0.15
rrl 1474639 n.982G>T non_coding_transcript_exon_variant 0.22
rrl 1474792 n.1135C>A non_coding_transcript_exon_variant 0.18
rrl 1475103 n.1446C>A non_coding_transcript_exon_variant 0.22
rrl 1475231 n.1574C>A non_coding_transcript_exon_variant 0.18
rrl 1475421 n.1764C>A non_coding_transcript_exon_variant 0.18
rrl 1475597 n.1940G>C non_coding_transcript_exon_variant 0.25
rrl 1475788 n.2131C>A non_coding_transcript_exon_variant 0.22
rrl 1476050 n.2393G>T non_coding_transcript_exon_variant 0.29
rrl 1476055 n.2398C>A non_coding_transcript_exon_variant 0.22
rrl 1476147 n.2490G>T non_coding_transcript_exon_variant 0.15
rrl 1476220 n.2563G>A non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>T non_coding_transcript_exon_variant 0.15
rrl 1476465 n.2808G>A non_coding_transcript_exon_variant 0.22
rrl 1476678 n.3021G>T non_coding_transcript_exon_variant 0.17
fabG1 1673410 c.-30C>G upstream_gene_variant 0.14
fabG1 1673521 c.84delG frameshift_variant 0.12
inhA 1674808 p.Val203Phe missense_variant 0.2
inhA 1674847 p.Gln216Lys missense_variant 0.18
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834303 c.762T>C synonymous_variant 0.13
rpsA 1834327 c.786G>C synonymous_variant 0.12
rpsA 1834355 p.Val272Leu missense_variant 0.12
rpsA 1834974 p.Ala478Gly missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918048 p.Leu37Met missense_variant 0.17
ndh 2102005 c.1038G>C synonymous_variant 0.14
ndh 2102319 p.Glu242Gln missense_variant 0.12
ndh 2102644 p.Glu133Asp missense_variant 0.14
ndh 2103076 c.-34C>G upstream_gene_variant 0.13
ndh 2103200 c.-158C>G upstream_gene_variant 0.17
katG 2154146 p.Asp656His missense_variant 0.12
katG 2154329 p.Arg595Gly missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155373 p.Asp247Tyr missense_variant 0.15
katG 2155899 c.213C>A synonymous_variant 0.17
katG 2156344 c.-233C>A upstream_gene_variant 0.18
katG 2156452 c.-341G>C upstream_gene_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169404 p.Asn403Lys missense_variant 0.17
PPE35 2170041 p.Thr191Lys missense_variant 0.17
Rv1979c 2222970 p.Phe65Leu missense_variant 0.14
Rv1979c 2223073 p.Gly31Val missense_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289733 c.-492G>T upstream_gene_variant 0.17
eis 2714480 p.Ala285Ser missense_variant 0.16
eis 2714565 c.768G>C synonymous_variant 0.14
eis 2714943 c.390C>A synonymous_variant 0.15
eis 2715156 c.177C>G synonymous_variant 0.12
eis 2715216 c.117G>T synonymous_variant 0.18
eis 2715303 p.Glu10Asp missense_variant 0.14
ahpC 2726580 p.Val130Leu missense_variant 0.17
folC 2747444 p.Ala52Glu missense_variant 0.18
folC 2747454 c.145C>A synonymous_variant 0.18
folC 2747490 p.Arg37Ser missense_variant 0.25
ribD 2986783 c.-56C>A upstream_gene_variant 0.15
ribD 2987487 p.Pro217Thr missense_variant 0.14
Rv2752c 3066005 p.Asp63Tyr missense_variant 0.18
Rv2752c 3066008 p.Pro62Ser missense_variant 0.18
Rv2752c 3066382 c.-191G>T upstream_gene_variant 0.18
thyX 3067351 p.Arg199Trp missense_variant 0.2
thyX 3067930 p.Pro6Thr missense_variant 0.2
thyX 3068009 c.-64G>T upstream_gene_variant 0.17
thyA 3074040 c.432G>C synonymous_variant 0.17
thyA 3074645 c.-174T>G upstream_gene_variant 0.31
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086997 p.Thr60Gly missense_variant 0.12
fbiD 3339729 c.612G>T synonymous_variant 0.18
fbiD 3339731 p.Pro205Leu missense_variant 0.18
Rv3083 3449926 p.Glu475Lys missense_variant 0.15
Rv3083 3449990 c.1487G>C stop_lost&splice_region_variant 0.12
fprA 3473856 c.-151C>G upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474628 p.Thr208Ala missense_variant 0.11
fprA 3474825 c.819C>G synonymous_variant 0.13
fprA 3474905 p.Gly300Ala missense_variant 1.0
fprA 3475251 c.1245G>T synonymous_variant 0.17
whiB7 3568762 c.-83G>T upstream_gene_variant 0.14
Rv3236c 3612182 p.Ala312Asp missense_variant 0.14
Rv3236c 3612512 p.Trp202Leu missense_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641975 c.441C>A synonymous_variant 0.17
fbiB 3641989 c.458delG frameshift_variant 0.14
fbiB 3642233 c.699G>A synonymous_variant 0.2
alr 3840912 p.Ala170Gly missense_variant 0.18
alr 3840941 c.480C>A synonymous_variant 0.2
rpoA 3878599 c.-92C>G upstream_gene_variant 0.12
ddn 3986686 c.-158G>T upstream_gene_variant 0.15
ddn 3986960 c.117C>A synonymous_variant 0.14
ddn 3986963 c.120C>A synonymous_variant 0.15
clpC1 4038884 c.1821C>A synonymous_variant 0.2
clpC1 4039834 p.Thr291Ala missense_variant 0.12
clpC1 4039990 p.Pro239Ser missense_variant 0.17
clpC1 4040011 p.Ala232Ser missense_variant 0.17
clpC1 4040220 p.Ser162Phe missense_variant 0.14
panD 4044439 c.-158G>C upstream_gene_variant 0.11
embC 4240271 p.Val137Leu missense_variant 0.12
embC 4240427 p.Ser189Gly missense_variant 0.18
embC 4240514 p.Val218Met missense_variant 0.14
embC 4241956 c.2094A>C synonymous_variant 0.12
embA 4242502 c.-731G>A upstream_gene_variant 0.17
embC 4242567 p.Thr902Asn missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4243002 p.Ser1047Ile missense_variant 0.18
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243497 p.Val89Leu missense_variant 0.15
embA 4243556 c.324C>T synonymous_variant 0.17
embA 4243604 c.372G>T synonymous_variant 0.15
embA 4243742 c.510T>C synonymous_variant 0.13
embA 4245680 p.Lys816Asn missense_variant 0.12
embA 4246290 p.Leu1020Ile missense_variant 0.15
embA 4246295 p.Trp1021Cys missense_variant 0.14
embB 4246545 p.Thr11Asn missense_variant 0.15
embB 4246559 c.50dupT frameshift_variant 0.14
embB 4246637 p.Val42Leu missense_variant 0.15
embB 4246781 p.Ala90Pro missense_variant 0.12
embB 4246897 c.384C>A synonymous_variant 0.18
embB 4247168 p.Leu219Met missense_variant 0.14
embB 4247228 c.715C>T synonymous_variant 0.4
embB 4247244 p.Gly244Val missense_variant 0.33
embB 4247271 p.Leu253Arg missense_variant 0.25
embB 4247282 c.769C>A synonymous_variant 0.2
embB 4247311 c.798C>A synonymous_variant 0.2
embB 4247886 p.Gly458Val missense_variant 0.15
embB 4248359 p.Pro616Ala missense_variant 0.11
embB 4248465 p.Ser651Ile missense_variant 0.2
embB 4248645 p.Ala711Gly missense_variant 0.11
embB 4249330 p.Met939Ile missense_variant 0.18
aftB 4267492 p.Ala449Ser missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268671 p.Glu56* stop_gained 0.18
aftB 4269369 c.-533G>C upstream_gene_variant 0.16
ubiA 4269458 p.Leu126Met missense_variant 0.15
ubiA 4269481 p.Trp118Ser missense_variant 0.13
ubiA 4269722 p.Ala38Ser missense_variant 0.14
ubiA 4269725 p.Leu37Met missense_variant 0.13
ethA 4328322 c.-849G>T upstream_gene_variant 0.15
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