TB-Profiler result

Run: ERR8665607
Summary

Run ID: ERR8665607

Sample name:

Date: 02-04-2023 07:33:45

Number of reads: 328105

Percentage reads mapped: 99.53

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761108 p.Met434Ile missense_variant 0.29 rifampicin
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
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 5301 p.Glu21Gly missense_variant 0.1
gyrB 6545 p.Gly436Cys missense_variant 0.33
gyrB 6650 p.Arg471Ser missense_variant 0.5
gyrB 6851 p.Gln538Lys missense_variant 0.29
gyrB 7097 p.Glu620* stop_gained 0.22
gyrA 7321 p.Pro7Gln missense_variant 0.2
gyrA 7324 p.Pro8His missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7469 c.168C>A synonymous_variant 0.25
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7624 p.Pro108Gln missense_variant 0.18
gyrA 7651 p.Gly117Asp missense_variant 0.14
gyrA 8450 p.Lys383Asn missense_variant 0.18
gyrA 8472 p.Leu391Met missense_variant 0.2
gyrA 8526 c.1225C>A synonymous_variant 0.22
gyrA 8578 p.Asp426Val missense_variant 0.15
gyrA 9222 p.Asp641Tyr missense_variant 0.33
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9567 p.Asp756Tyr missense_variant 0.25
gyrA 9632 c.2331C>A synonymous_variant 0.2
fgd1 490584 c.-199C>A upstream_gene_variant 0.22
fgd1 490592 c.-191C>A upstream_gene_variant 0.29
fgd1 490670 c.-113G>T upstream_gene_variant 0.25
fgd1 491157 p.Phe125Leu missense_variant 0.22
fgd1 491311 p.Gly177Cys missense_variant 0.5
fgd1 491321 p.Ala180Val missense_variant 0.5
fgd1 491580 c.798C>A synonymous_variant 0.29
fgd1 491652 c.870C>A synonymous_variant 0.25
fgd1 491685 c.903G>T synonymous_variant 0.67
mshA 575588 p.Arg81Ser missense_variant 0.33
mshA 575591 c.244C>A synonymous_variant 0.22
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576322 c.975G>T synonymous_variant 0.5
ccsA 620026 p.Pro46Thr missense_variant 0.5
ccsA 620118 c.228C>A synonymous_variant 0.5
ccsA 620167 p.Ala93Ser missense_variant 0.67
ccsA 620171 p.Cys94Tyr missense_variant 0.67
ccsA 620384 p.Pro165Gln missense_variant 0.22
ccsA 620396 p.Ser169Tyr missense_variant 0.2
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759662 c.-145C>T upstream_gene_variant 0.22
rpoB 760124 p.Phe106Leu missense_variant 0.4
rpoB 760301 c.495C>A synonymous_variant 0.2
rpoB 760400 c.594G>T synonymous_variant 0.33
rpoB 761573 c.1767C>A synonymous_variant 0.33
rpoB 761598 p.Arg598Ser missense_variant 0.22
rpoB 762651 p.Trp949Arg missense_variant 0.29
rpoC 762680 c.-690C>A upstream_gene_variant 0.25
rpoC 762794 c.-576C>A upstream_gene_variant 0.29
rpoB 763001 p.Met1065Ile missense_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763116 p.Glu1104* stop_gained 0.27
rpoC 763637 p.Glu90* stop_gained 0.29
rpoC 763646 p.Gly93Cys missense_variant 0.29
rpoC 763834 p.Met155Ile missense_variant 0.33
rpoC 764449 c.1080G>T synonymous_variant 0.4
rpoC 764579 p.Asp404Tyr missense_variant 0.22
rpoC 764669 p.Pro434Thr missense_variant 0.22
rpoC 764770 p.Gln467His missense_variant 0.18
rpoC 764817 p.Val483Ala missense_variant 1.0
rpoC 764965 p.Phe532Leu missense_variant 0.22
rpoC 765343 c.1974G>T synonymous_variant 0.4
rpoC 765808 p.Gln813His missense_variant 0.4
rpoC 766199 c.2830C>T synonymous_variant 0.2
rpoC 766223 p.Leu952Met missense_variant 0.25
rpoC 766260 p.Ser964* stop_gained 0.25
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 766744 p.Gln1125His missense_variant 0.2
rpoC 766982 p.Pro1205Thr missense_variant 0.4
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776162 c.2319C>A synonymous_variant 0.2
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776552 p.Gln643His missense_variant 0.33
mmpL5 777260 c.1221C>A synonymous_variant 0.29
mmpL5 777876 p.Arg202Leu missense_variant 0.22
mmpL5 778621 c.-141G>T upstream_gene_variant 0.33
mmpR5 779023 p.Ala12Tyr missense_variant 0.22
mmpR5 779315 p.Arg109Leu missense_variant 0.29
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781501 c.-59C>A upstream_gene_variant 0.6
rpsL 781651 p.Arg31His missense_variant 0.25
rplC 801219 c.411C>A synonymous_variant 0.4
rplC 801416 p.Gly203Val missense_variant 0.17
rplC 801444 c.636C>A synonymous_variant 0.22
fbiC 1302958 p.Thr10Ser missense_variant 0.22
fbiC 1303237 p.His103Asp missense_variant 0.14
fbiC 1304578 p.Arg550Ser missense_variant 0.4
fbiC 1304592 p.Phe554Leu missense_variant 0.29
fbiC 1305080 p.Arg717Leu missense_variant 0.25
Rv1258c 1406677 p.Leu222Met missense_variant 0.33
Rv1258c 1406722 p.Gly207Trp missense_variant 0.25
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417099 c.249C>T synonymous_variant 0.25
embR 1417160 p.Trp63Leu missense_variant 0.2
embR 1417257 p.Gly31Cys missense_variant 0.29
embR 1417439 c.-92G>T upstream_gene_variant 0.2
atpE 1461249 p.Ala69Ser missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472343 n.498C>A non_coding_transcript_exon_variant 0.18
rrs 1472976 n.1131G>T non_coding_transcript_exon_variant 0.19
rrs 1473172 n.1327T>C non_coding_transcript_exon_variant 0.14
rrl 1474648 n.991G>T non_coding_transcript_exon_variant 0.2
rrl 1475034 n.1377G>T non_coding_transcript_exon_variant 0.18
rrl 1475047 n.1390G>T non_coding_transcript_exon_variant 0.17
fabG1 1673272 c.-168C>T upstream_gene_variant 0.17
fabG1 1673436 c.-4C>A upstream_gene_variant 0.33
inhA 1674260 p.Ser20* stop_gained 0.25
inhA 1674957 c.756G>T synonymous_variant 0.22
rpsA 1833447 c.-95C>A upstream_gene_variant 0.2
rpsA 1834029 p.Pro163His missense_variant 0.18
rpsA 1834036 c.495C>A synonymous_variant 0.27
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834519 c.978G>T synonymous_variant 0.22
rpsA 1834542 p.Pro334His missense_variant 0.33
rpsA 1834544 p.Asp335Tyr missense_variant 0.22
rpsA 1834752 p.Leu404Pro missense_variant 0.33
tlyA 1917923 c.-17G>T upstream_gene_variant 0.29
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101810 c.1233C>A synonymous_variant 0.2
ndh 2101816 c.1227C>A synonymous_variant 0.36
ndh 2101846 c.1197G>A synonymous_variant 0.2
ndh 2101867 c.1176C>A synonymous_variant 0.22
katG 2154278 p.Asp612Tyr missense_variant 0.27
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155663 p.Pro150Gln missense_variant 0.5
katG 2155957 p.Pro52Gln missense_variant 0.18
katG 2156256 c.-145C>A upstream_gene_variant 0.29
katG 2156341 c.-230G>T upstream_gene_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168240 c.2373C>A synonymous_variant 0.25
PPE35 2169146 c.1467G>T synonymous_variant 0.2
PPE35 2169283 p.Arg444Ser missense_variant 0.22
Rv1979c 2222695 p.Arg157Leu missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289378 c.-137G>T upstream_gene_variant 0.23
kasA 2518418 p.Glu102* stop_gained 0.29
kasA 2518541 p.Gln143Lys missense_variant 0.25
kasA 2518549 c.435C>A synonymous_variant 0.2
kasA 2518564 c.450C>A synonymous_variant 0.22
kasA 2519308 c.1194C>A synonymous_variant 0.2
ahpC 2726232 p.Gln14Lys missense_variant 0.23
ahpC 2726513 c.321C>A synonymous_variant 0.18
folC 2746376 p.Ser408* stop_gained 0.29
folC 2747026 c.573C>A synonymous_variant 0.25
folC 2747103 p.Ala166Ser missense_variant 0.17
folC 2747273 p.Ser109* stop_gained 0.22
folC 2747287 c.312G>T synonymous_variant 0.22
folC 2747344 c.255G>T synonymous_variant 0.25
pepQ 2859599 p.Asp274Tyr missense_variant 0.67
pepQ 2859722 p.Met233Val missense_variant 0.33
pepQ 2860484 c.-66G>T upstream_gene_variant 0.29
ribD 2987138 c.300C>A synonymous_variant 0.5
ribD 2987285 c.447C>A synonymous_variant 0.22
thyX 3067590 p.Pro119Gln missense_variant 0.29
thyX 3067823 c.123G>T synonymous_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087758 c.939G>T synonymous_variant 0.29
Rv3083 3449324 p.Arg274Leu missense_variant 0.25
fprA 3473836 c.-171C>A upstream_gene_variant 0.38
fprA 3473874 c.-133C>A upstream_gene_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474492 c.486G>T synonymous_variant 0.18
fprA 3475140 c.1134C>A synonymous_variant 0.22
fprA 3475294 p.Glu430* stop_gained 0.4
whiB7 3568478 p.Gly68Cys missense_variant 0.22
Rv3236c 3612025 c.1092C>A synonymous_variant 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3641537 c.3G>T start_lost 0.67
fbiB 3641736 p.Glu68* stop_gained 0.25
fbiB 3641749 p.Arg72Leu missense_variant 0.25
fbiB 3641753 p.Leu73Phe missense_variant 0.29
fbiB 3642362 c.828C>A synonymous_variant 0.33
fbiB 3642470 c.936G>T synonymous_variant 0.25
fbiB 3642484 p.Trp317Leu missense_variant 0.29
alr 3840316 p.Gly369Cys missense_variant 0.25
alr 3840464 p.Phe319Leu missense_variant 0.5
alr 3840619 p.Asp268Tyr missense_variant 0.29
alr 3840646 p.Gly259Trp missense_variant 0.2
rpoA 3877691 p.Gly273Cys missense_variant 0.33
rpoA 3878582 c.-75C>A upstream_gene_variant 0.25
ddn 3987235 p.Pro131Gln missense_variant 0.22
clpC1 4039475 p.Met410Ile missense_variant 0.22
clpC1 4040549 p.Leu52Phe missense_variant 0.2
embC 4241274 p.Pro471Gln missense_variant 0.29
embC 4241318 p.Pro486Thr missense_variant 0.25
embC 4241330 p.Asp490Tyr missense_variant 0.25
embC 4241581 c.1719C>A synonymous_variant 0.22
embC 4242034 c.2172C>A synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243451 c.219G>T synonymous_variant 0.29
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243763 c.531G>T synonymous_variant 0.67
embA 4243766 p.Lys178Asn missense_variant 0.67
embA 4244669 c.1437G>T synonymous_variant 0.2
embA 4245086 c.1854C>A synonymous_variant 0.17
embA 4245308 c.2076G>T synonymous_variant 0.25
embA 4245724 p.Gly831Val missense_variant 0.22
embA 4246153 p.Ala974Val missense_variant 0.25
embB 4246352 c.-162G>T upstream_gene_variant 0.25
embA 4246394 p.Trp1054Cys missense_variant 0.2
embB 4246403 c.-111G>T upstream_gene_variant 0.18
embA 4246417 p.Arg1062Leu missense_variant 0.2
embB 4246587 p.Gly25Val missense_variant 0.29
embB 4247215 c.702C>A synonymous_variant 0.33
embB 4247707 p.Phe398Leu missense_variant 0.33
embB 4248012 p.Ser500* stop_gained 0.22
embB 4248041 p.Ala510Ser missense_variant 0.25
embB 4248050 p.Gly513Trp missense_variant 0.25
embB 4248723 p.Trp737Leu missense_variant 0.22
embB 4248745 c.2232C>T synonymous_variant 0.22
embB 4248775 c.2262C>A synonymous_variant 0.22
aftB 4267131 p.Pro569Arg missense_variant 0.17
aftB 4267216 p.Gly541* stop_gained 0.22
aftB 4267219 p.Asp540Tyr missense_variant 0.22
aftB 4267238 p.Phe533Leu missense_variant 0.33
aftB 4267373 c.1463delT frameshift_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268610 p.Pro76Gln missense_variant 0.22
aftB 4268707 p.Gly44Cys missense_variant 0.33
ethA 4326383 p.Thr364Asn missense_variant 0.15
ethA 4326498 p.Arg326Trp missense_variant 0.18
ethA 4326503 p.Gly324Val missense_variant 0.18
ethA 4326593 p.Cys294Phe missense_variant 1.0
ethR 4326901 c.-648C>A upstream_gene_variant 0.22
ethA 4327471 c.3G>T start_lost 0.2
ethR 4327777 p.Asp77Tyr missense_variant 0.2
ethR 4327780 p.Arg78Trp missense_variant 0.22
ethA 4328133 c.-660C>A upstream_gene_variant 0.18
ethA 4328212 c.-739G>T upstream_gene_variant 0.2
ethA 4328226 c.-753G>T upstream_gene_variant 0.22
ethA 4328245 c.-772C>A upstream_gene_variant 0.18
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
gid 4408013 c.190C>A synonymous_variant 0.18
gid 4408093 p.Gly37Val missense_variant 0.2
gid 4408117 p.Pro29His missense_variant 0.18
gid 4408195 p.Pro3Leu missense_variant 0.25
gid 4408343 c.-141C>A upstream_gene_variant 0.25