TB-Profiler result

Run: ERR8665609
Summary

Run ID: ERR8665609

Sample name:

Date: 02-04-2023 07:33:44

Number of reads: 323144

Percentage reads mapped: 99.5

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 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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288766 p.Leu159Arg missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
embB 4247703 p.Pro397Gln missense_variant 0.38 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 5081 c.-159G>T upstream_gene_variant 0.2
gyrB 5149 c.-91G>T upstream_gene_variant 0.18
gyrB 5158 c.-82G>T upstream_gene_variant 0.2
gyrB 5572 c.333G>T synonymous_variant 0.29
gyrB 5912 p.Asp225Tyr missense_variant 0.29
gyrB 6494 p.Ala419Thr missense_variant 0.33
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7512 p.Ala71Ser missense_variant 0.2
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7706 c.405C>A synonymous_variant 0.33
gyrA 7747 p.Thr149Ile missense_variant 0.33
gyrA 7751 c.450C>A synonymous_variant 0.29
gyrA 7982 p.Asp227Glu missense_variant 0.33
gyrA 8664 p.Leu455Met missense_variant 0.29
gyrA 9008 p.Phe569Leu missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9810 p.Gly837Cys missense_variant 0.29
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575199 c.-149G>A upstream_gene_variant 0.5
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576105 p.Arg253Leu missense_variant 0.18
mshA 576140 p.Glu265* stop_gained 0.2
mshA 576246 p.Gly300Ala missense_variant 0.5
mshA 576413 p.Gly356Cys missense_variant 0.29
ccsA 619953 c.63C>A synonymous_variant 0.29
ccsA 620316 c.426G>T synonymous_variant 0.25
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620667 p.Trp259Cys missense_variant 0.29
rpoB 759849 p.Pro15Thr missense_variant 0.19
rpoB 759971 p.Phe55Leu missense_variant 0.21
rpoB 760229 c.423C>A synonymous_variant 0.5
rpoB 760977 p.Glu391* stop_gained 0.33
rpoB 761000 p.Met398Ile missense_variant 0.29
rpoB 761829 p.Gly675Cys missense_variant 0.29
rpoB 761891 c.2085G>T synonymous_variant 0.33
rpoB 762054 p.Glu750* stop_gained 0.4
rpoB 762215 p.Lys803Asn missense_variant 0.2
rpoB 762566 p.Met920Ile missense_variant 0.29
rpoB 762930 p.Pro1042Thr missense_variant 0.14
rpoB 763026 p.Gly1074Cys missense_variant 0.29
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763556 p.Gly63Cys missense_variant 0.25
rpoC 763585 c.216C>T synonymous_variant 0.4
rpoC 764479 p.Glu370Asp missense_variant 0.33
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 765262 c.1893C>A synonymous_variant 0.2
rpoC 766286 p.Gly973Ser missense_variant 0.5
rpoC 766346 p.Glu993Lys missense_variant 0.25
rpoC 766645 p.Glu1092Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776045 c.2436G>T synonymous_variant 0.25
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776150 p.Met777Ile missense_variant 0.33
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776343 p.Gly713Val missense_variant 0.2
mmpL5 777795 p.Ser229* stop_gained 0.29
mmpL5 778010 p.Gln157His missense_variant 0.25
mmpR5 779413 p.Leu142Met missense_variant 0.25
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781716 p.Ala53Ser missense_variant 0.17
rpsL 781730 p.Leu57Phe missense_variant 0.2
rplC 800952 c.144C>T synonymous_variant 0.25
fbiC 1303375 p.Asp149Tyr missense_variant 0.22
fbiC 1304266 c.1336C>A synonymous_variant 0.2
fbiC 1304835 c.1905G>T synonymous_variant 0.25
Rv1258c 1406280 p.Ser354* stop_gained 0.22
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407371 c.-31C>A upstream_gene_variant 0.18
embR 1416808 c.540C>A synonymous_variant 0.2
atpE 1461035 c.-10G>T upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472548 n.703A>G non_coding_transcript_exon_variant 0.15
rrs 1472766 n.921G>A non_coding_transcript_exon_variant 0.2
rrl 1473515 n.-143G>T upstream_gene_variant 0.21
rrl 1473925 n.268G>T non_coding_transcript_exon_variant 0.15
rrl 1474063 n.406G>T non_coding_transcript_exon_variant 0.2
rrl 1474408 n.751G>T non_coding_transcript_exon_variant 0.4
rrl 1474757 n.1100C>A non_coding_transcript_exon_variant 0.2
rrl 1474928 n.1271C>A non_coding_transcript_exon_variant 0.25
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.2
inhA 1673685 c.-517C>A upstream_gene_variant 0.3
inhA 1674939 c.738G>T synonymous_variant 0.18
rpsA 1833628 c.87G>C synonymous_variant 0.17
rpsA 1833883 c.342C>A synonymous_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834480 c.939C>A synonymous_variant 0.29
rpsA 1834522 c.981C>A synonymous_variant 0.25
rpsA 1834598 p.Leu353Met missense_variant 0.25
rpsA 1834890 p.Ser450* stop_gained 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918686 c.747G>T synonymous_variant 0.33
ndh 2101746 p.Asp433Tyr missense_variant 0.25
ndh 2101987 c.1056C>A synonymous_variant 0.25
ndh 2102692 c.351C>A synonymous_variant 0.33
katG 2153975 p.Ala713Thr missense_variant 0.33
katG 2153988 c.2124C>A synonymous_variant 0.4
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155166 p.Gly316Cys missense_variant 0.29
katG 2156050 p.Pro21His missense_variant 0.33
katG 2156244 c.-133G>C upstream_gene_variant 0.15
katG 2156283 c.-172G>T upstream_gene_variant 0.4
katG 2156534 c.-423G>T upstream_gene_variant 0.25
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168642 p.Phe657Leu missense_variant 0.23
PPE35 2169251 c.1362C>A synonymous_variant 0.22
PPE35 2169804 p.Ala270Glu missense_variant 0.29
PPE35 2170182 p.Trp144Leu missense_variant 0.33
PPE35 2170555 p.Gly20Cys missense_variant 0.22
Rv1979c 2221797 p.Phe456Leu missense_variant 0.42
Rv1979c 2221816 p.Ala450Asp missense_variant 0.15
Rv1979c 2221929 p.Phe412Leu missense_variant 0.22
Rv1979c 2222016 p.Phe383Leu missense_variant 0.29
Rv1979c 2222022 c.1143C>A synonymous_variant 0.29
Rv1979c 2222245 p.Gly307Val missense_variant 0.22
Rv1979c 2222309 p.Asp286Tyr missense_variant 0.18
Rv1979c 2222339 p.Leu276Met missense_variant 0.25
Rv1979c 2222797 p.Pro123His missense_variant 0.25
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289270 c.-29G>T upstream_gene_variant 0.22
pncA 2290038 c.-797G>T upstream_gene_variant 0.2
pncA 2290062 c.-821G>T upstream_gene_variant 0.22
kasA 2518804 p.Phe230Leu missense_variant 0.25
eis 2714487 c.846C>A synonymous_variant 0.29
eis 2715156 c.177C>A synonymous_variant 0.29
ahpC 2726529 p.Asp113Tyr missense_variant 0.4
folC 2746636 c.963C>A synonymous_variant 0.5
folC 2747209 p.Leu130Phe missense_variant 0.5
folC 2747402 p.Ser66* stop_gained 0.25
pepQ 2859593 p.Ala276Ser missense_variant 0.25
pepQ 2859603 p.Gly272Cys missense_variant 0.18
pepQ 2859659 p.Ala254Ser missense_variant 0.18
pepQ 2859799 p.Pro207Gln missense_variant 0.33
pepQ 2860343 p.Asp26Tyr missense_variant 0.22
pepQ 2860369 p.Ser17Tyr missense_variant 0.29
pepQ 2860376 p.Ala15Thr missense_variant 0.33
ribD 2986794 c.-45G>T upstream_gene_variant 0.2
ribD 2986829 c.-10A>G upstream_gene_variant 0.18
ribD 2986911 p.Asp25Tyr missense_variant 0.33
Rv2752c 3065148 c.1044C>A synonymous_variant 0.22
Rv2752c 3065152 p.Ala347Val missense_variant 0.22
Rv2752c 3065228 p.Glu322* stop_gained 0.43
Rv2752c 3065301 c.891C>A synonymous_variant 0.33
Rv2752c 3065554 p.Pro213Gln missense_variant 0.29
Rv2752c 3065673 p.Phe173Leu missense_variant 0.4
Rv2752c 3065788 p.Arg135Leu missense_variant 0.33
Rv2752c 3066007 p.Pro62Gln missense_variant 0.22
thyA 3073862 p.Gly204Cys missense_variant 0.25
thyA 3074290 p.Trp61Leu missense_variant 0.23
ald 3086712 c.-108C>A upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087503 c.684C>A synonymous_variant 0.25
ald 3087676 p.Pro286Arg missense_variant 0.12
fbiD 3339382 p.Pro89Thr missense_variant 0.18
Rv3083 3448476 c.-28G>T upstream_gene_variant 0.25
Rv3083 3448489 c.-15C>T upstream_gene_variant 0.29
Rv3083 3448731 c.228C>A synonymous_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474815 p.Arg270Leu missense_variant 0.22
fprA 3474835 p.Glu277* stop_gained 0.25
fprA 3475265 p.Ser420* stop_gained 0.33
fprA 3475313 p.Pro436Gln missense_variant 0.33
whiB7 3568435 p.Pro82Gln missense_variant 0.25
whiB7 3568463 p.Gln73Lys missense_variant 0.22
whiB7 3568650 c.30C>G synonymous_variant 0.33
whiB7 3568777 c.-98C>A upstream_gene_variant 0.29
Rv3236c 3611965 c.1152G>T synonymous_variant 0.25
Rv3236c 3612370 c.747C>A synonymous_variant 0.25
Rv3236c 3612550 c.567C>T synonymous_variant 0.25
Rv3236c 3612575 p.Ala181Glu missense_variant 0.22
Rv3236c 3612634 c.483G>T synonymous_variant 0.25
Rv3236c 3612646 c.471C>A synonymous_variant 0.4
Rv3236c 3612880 c.237G>T synonymous_variant 0.67
fbiB 3640887 c.-648C>A upstream_gene_variant 0.22
alr 3840340 p.Asp361Asn missense_variant 0.22
alr 3840383 p.Phe346Leu missense_variant 0.29
alr 3840763 p.Ala220Ser missense_variant 0.67
rpoA 3877532 p.Ala326Thr missense_variant 0.25
rpoA 3877533 c.975C>A synonymous_variant 0.25
rpoA 3878352 c.156C>A synonymous_variant 0.2
rpoA 3878355 c.153C>A synonymous_variant 0.2
ddn 3987260 p.Trp139Cys missense_variant 0.18
clpC1 4038883 p.Gly608Cys missense_variant 0.18
clpC1 4039025 c.1680C>A synonymous_variant 0.2
clpC1 4039660 p.Glu349* stop_gained 0.2
clpC1 4039690 p.Glu339* stop_gained 0.22
clpC1 4039907 p.Glu266Asp missense_variant 0.2
clpC1 4040746 c.-42C>A upstream_gene_variant 0.25
panD 4044065 p.Gly73Cys missense_variant 0.2
panD 4044089 p.Gly65Cys missense_variant 0.22
embC 4239899 c.37C>A synonymous_variant 0.18
embC 4240665 p.Trp268Leu missense_variant 0.25
embC 4240739 p.Asp293Tyr missense_variant 0.4
embC 4241709 p.Arg616Leu missense_variant 0.33
embC 4241981 p.Pro707Thr missense_variant 0.22
embC 4242426 p.Arg855Leu missense_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242816 p.Trp985Leu missense_variant 0.25
embA 4243238 c.6C>A synonymous_variant 0.5
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243589 c.357C>A synonymous_variant 0.5
embA 4244124 p.Gly298Cys missense_variant 0.29
embA 4244239 p.Trp336* stop_gained 0.29
embA 4244672 c.1440C>A synonymous_variant 0.29
embA 4245029 p.Ser599Arg missense_variant 0.17
embB 4245794 c.-720G>T upstream_gene_variant 0.33
embA 4245962 p.Gln910His missense_variant 0.67
embA 4246065 p.Asp945Tyr missense_variant 0.25
embA 4246146 p.Gly972Trp missense_variant 0.33
embA 4246204 p.Arg991Leu missense_variant 0.33
embB 4247633 p.Gly374Arg missense_variant 0.29
embB 4247688 p.Leu392Pro missense_variant 0.22
embB 4249560 p.Pro1016Gln missense_variant 0.2
embB 4249796 c.3283C>A synonymous_variant 0.4
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267735 p.Gly368Cys missense_variant 0.22
aftB 4268164 p.Gln225* stop_gained 0.25
ubiA 4269224 p.Ala204Ser missense_variant 0.22
aftB 4269228 c.-392C>T upstream_gene_variant 0.22
ubiA 4269294 p.Met180Ile missense_variant 0.5
ethA 4326141 p.Glu445* stop_gained 0.4
ethA 4326593 p.Cys294Phe missense_variant 1.0
ethR 4327781 p.Arg78Gln missense_variant 0.22
ethR 4328134 p.Glu196* stop_gained 0.29
whiB6 4338175 p.Ala116Val missense_variant 0.29
whiB6 4338450 c.72C>A synonymous_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338621 c.-100G>T upstream_gene_variant 0.18
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407701 p.His168Asn missense_variant 0.25
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407970 p.Pro78Gln missense_variant 0.18
gid 4408089 c.114C>A synonymous_variant 0.25
gid 4408124 p.Ala27Ser missense_variant 0.22