TB-Profiler result

Run: ERR4828518
Summary

Run ID: ERR4828518

Sample name:

Date: 01-04-2023 18:55:43

Number of reads: 648171

Percentage reads mapped: 62.13

Strain: lineage2.2.1

Drug-resistance: HR-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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.2 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288730 p.Ala171Val missense_variant 0.33 pyrazinamide
embB 4247703 p.Pro397Gln missense_variant 0.15 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 5246 c.10delC frameshift_variant 0.12
gyrB 5428 c.189C>A synonymous_variant 0.2
gyrB 5488 c.249C>A synonymous_variant 0.17
gyrB 5822 p.Gln195* stop_gained 0.17
gyrB 6284 p.Asp349Tyr missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7931 c.630C>A synonymous_variant 0.17
gyrA 8355 p.Val352Met missense_variant 0.15
gyrA 8395 p.Tyr365Ser missense_variant 0.1
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9630 p.Val777Ile missense_variant 0.17
gyrA 9661 p.Ala787Val missense_variant 0.15
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576395 p.Ser350Cys missense_variant 0.29
mshA 576571 p.Leu408Phe missense_variant 0.2
ccsA 620011 p.Gly41Ser missense_variant 0.2
ccsA 620304 p.Trp138Cys missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759653 c.-154C>T upstream_gene_variant 0.14
rpoB 759977 p.Trp57* stop_gained 0.2
rpoB 760065 c.259C>T synonymous_variant 0.22
rpoB 760873 p.Glu356Gly missense_variant 0.22
rpoB 761401 p.Arg532His missense_variant 0.17
rpoB 761921 c.2115C>T synonymous_variant 0.22
rpoB 762151 p.Gly782Val missense_variant 0.4
rpoB 762378 p.Gly858Ser missense_variant 0.15
rpoC 762446 c.-924C>T upstream_gene_variant 0.18
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763632 p.Arg88His missense_variant 0.18
rpoC 763635 p.Arg89His missense_variant 0.18
rpoC 763664 p.Ala99Thr missense_variant 0.22
rpoC 764367 p.Gly333Asp missense_variant 0.15
rpoC 765004 c.1635G>T synonymous_variant 0.25
rpoC 765142 p.Glu591Asp missense_variant 0.18
rpoC 766141 c.2772C>T synonymous_variant 0.15
rpoC 766187 p.Arg940Cys missense_variant 0.2
rpoC 766280 p.Ser971Arg missense_variant 0.14
rpoC 766319 p.Ala984Thr missense_variant 0.14
rpoC 766640 p.His1091Tyr missense_variant 0.17
rpoC 766916 p.Arg1183Ser missense_variant 0.15
mmpL5 775608 p.Ala958Val missense_variant 0.17
mmpL5 775610 c.2871G>A synonymous_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 0.9
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776296 p.Gln729Lys missense_variant 0.15
mmpL5 776411 c.2070T>C synonymous_variant 0.12
mmpL5 776442 p.Phe680Ser missense_variant 0.11
mmpL5 777025 c.1456C>A synonymous_variant 0.18
mmpL5 777309 p.Gly391Val missense_variant 0.33
mmpL5 777751 p.Arg244Ser missense_variant 0.17
mmpR5 778322 c.-668C>T upstream_gene_variant 0.18
mmpL5 778931 c.-451A>T upstream_gene_variant 0.14
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800904 c.99delC frameshift_variant 0.12
rplC 801025 p.Ala73Ser missense_variant 0.22
fbiC 1303004 p.Ala25Val missense_variant 0.29
fbiC 1303043 p.Thr38Met missense_variant 0.25
fbiC 1303475 p.Leu182Pro missense_variant 0.12
fbiC 1303575 c.645G>C synonymous_variant 0.15
fbiC 1303605 c.675C>G synonymous_variant 0.33
fbiC 1304106 c.1176G>T synonymous_variant 0.17
fbiC 1304887 p.Leu653Met missense_variant 0.18
fbiC 1305014 p.Thr695Met missense_variant 0.18
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407080 c.261C>A synonymous_variant 0.17
embR 1416520 c.828G>T synonymous_variant 0.17
embR 1416529 c.819C>T synonymous_variant 0.25
embR 1417147 c.201C>A synonymous_variant 0.15
embR 1417164 p.Glu62* stop_gained 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472176 n.331G>T non_coding_transcript_exon_variant 0.18
rrs 1472203 n.358G>T non_coding_transcript_exon_variant 0.18
rrs 1472257 n.412G>T non_coding_transcript_exon_variant 0.18
rrs 1472301 n.456C>T non_coding_transcript_exon_variant 0.2
rrs 1472374 n.529T>C non_coding_transcript_exon_variant 0.18
rrs 1472438 n.593T>A non_coding_transcript_exon_variant 0.22
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.25
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.25
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.25
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.29
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.29
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.29
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.33
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.29
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.29
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.29
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.33
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.33
rrs 1472596 n.751G>T non_coding_transcript_exon_variant 0.4
rrs 1472598 n.753A>T non_coding_transcript_exon_variant 0.4
rrs 1472614 n.769G>T non_coding_transcript_exon_variant 0.43
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.43
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.43
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.33
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.2
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.2
rrs 1472780 n.935G>A non_coding_transcript_exon_variant 0.29
rrs 1473135 n.1290C>T non_coding_transcript_exon_variant 0.17
rrs 1473148 n.1303G>T non_coding_transcript_exon_variant 0.17
rrs 1473233 n.1388C>A non_coding_transcript_exon_variant 0.33
rrl 1473734 n.77C>A non_coding_transcript_exon_variant 0.2
rrl 1473907 n.250G>T non_coding_transcript_exon_variant 0.29
rrl 1474208 n.551C>T non_coding_transcript_exon_variant 0.29
rrl 1475076 n.1419C>T non_coding_transcript_exon_variant 0.18
rrl 1475079 n.1423delG non_coding_transcript_exon_variant 0.17
rrl 1475139 n.1482C>T non_coding_transcript_exon_variant 0.15
rrl 1475602 n.1945G>A non_coding_transcript_exon_variant 0.17
rrl 1475722 n.2065G>A non_coding_transcript_exon_variant 0.15
rrl 1476178 n.2521C>T non_coding_transcript_exon_variant 0.33
rrl 1476180 n.2523C>T non_coding_transcript_exon_variant 0.33
rrl 1476546 n.2889C>A non_coding_transcript_exon_variant 0.29
fabG1 1673693 p.Leu85Pro missense_variant 0.14
inhA 1674177 c.-25C>A upstream_gene_variant 0.14
rpsA 1833404 c.-138G>T upstream_gene_variant 0.2
rpsA 1833723 p.Gly61Val missense_variant 0.29
rpsA 1833769 c.228C>A synonymous_variant 0.18
rpsA 1834105 c.564C>T synonymous_variant 0.29
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834432 c.891G>A synonymous_variant 0.22
rpsA 1834824 p.His428Arg missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102017 c.1026C>T synonymous_variant 0.17
ndh 2102198 p.Ala282Asp missense_variant 0.18
ndh 2102390 p.Pro218Leu missense_variant 0.25
ndh 2102448 p.Gly199Ser missense_variant 0.22
katG 2154210 c.1902C>T synonymous_variant 0.2
katG 2154602 p.Gly504Trp missense_variant 0.18
katG 2154672 c.1440G>T synonymous_variant 0.17
katG 2154683 p.Trp477Arg missense_variant 0.15
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156042 p.Gly24Ser missense_variant 0.2
PPE35 2167837 p.Gly926Trp missense_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167995 p.Ser873Asn missense_variant 0.18
PPE35 2169339 p.Gly425Asp missense_variant 0.15
PPE35 2169394 p.Ala407Thr missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289167 c.75C>T synonymous_variant 0.17
kasA 2518780 p.Glu222Asp missense_variant 0.18
eis 2714670 p.Asp221Glu missense_variant 0.22
eis 2715138 p.Met65Ile missense_variant 0.17
eis 2715148 p.Ala62Glu missense_variant 0.18
eis 2715408 c.-76G>T upstream_gene_variant 0.15
ahpC 2726334 p.Arg48Trp missense_variant 0.18
ahpC 2726417 c.225C>T synonymous_variant 0.22
folC 2746300 c.1299C>A synonymous_variant 0.18
folC 2746303 c.1296C>A synonymous_variant 0.18
folC 2746870 p.Glu243Asp missense_variant 0.15
folC 2746947 p.Gly218Cys missense_variant 0.15
folC 2746967 p.Gly211Val missense_variant 0.18
folC 2747204 p.Ala132Val missense_variant 0.18
folC 2747367 p.Val78Leu missense_variant 0.29
folC 2747763 c.-165G>T upstream_gene_variant 0.17
folC 2747783 c.-185G>T upstream_gene_variant 0.22
pepQ 2859602 p.Val273Leu missense_variant 0.15
pepQ 2859621 c.798G>T synonymous_variant 0.17
pepQ 2859774 c.645C>A synonymous_variant 0.14
pepQ 2859813 c.606C>A synonymous_variant 0.18
pepQ 2860151 p.Ala90Ser missense_variant 0.17
Rv2752c 3064702 p.Phe497Ser missense_variant 0.14
Rv2752c 3065030 p.Val388Leu missense_variant 0.22
Rv2752c 3067026 c.-835C>A upstream_gene_variant 0.22
thyX 3068073 c.-128C>T upstream_gene_variant 0.18
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087538 p.Leu240Pro missense_variant 0.25
ald 3087585 p.Ala256Thr missense_variant 0.33
ald 3087652 p.Ser278Leu missense_variant 0.15
fbiD 3339420 c.303C>A synonymous_variant 0.17
fbiD 3339472 p.Ala119Thr missense_variant 0.14
Rv3083 3448564 p.Cys21Ser missense_variant 0.25
Rv3083 3448788 c.285C>T synonymous_variant 0.17
Rv3083 3449137 p.Arg212* stop_gained 0.29
Rv3083 3449542 p.Gly347Ser missense_variant 0.24
Rv3083 3449586 c.1083C>T synonymous_variant 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474210 c.204A>G synonymous_variant 0.12
fprA 3474448 p.Ala148Thr missense_variant 0.2
fprA 3474768 c.762C>G synonymous_variant 0.22
fprA 3475045 c.1039C>A synonymous_variant 0.2
fprA 3475243 p.Arg413Cys missense_variant 0.17
fprA 3475366 p.Gly454Trp missense_variant 0.22
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613285 c.-169C>A upstream_gene_variant 0.33
fbiA 3640358 c.-185C>A upstream_gene_variant 0.14
fbiA 3640372 c.-171A>G upstream_gene_variant 0.71
fbiA 3640488 c.-55G>T upstream_gene_variant 0.15
fbiA 3640751 p.Gly70Asp missense_variant 0.22
fbiA 3641339 p.Asp266Gly missense_variant 0.13
fbiB 3641373 c.-162C>A upstream_gene_variant 0.18
fbiB 3641385 c.-150C>A upstream_gene_variant 0.17
fbiA 3641509 p.Gly323Arg missense_variant 0.25
fbiB 3641655 p.Arg41Cys missense_variant 0.18
fbiB 3641734 p.Pro67Leu missense_variant 0.21
fbiB 3642008 c.474C>T synonymous_variant 0.15
fbiB 3642056 c.522C>T synonymous_variant 0.17
fbiB 3642623 c.1089C>T synonymous_variant 0.25
fbiB 3642656 c.1122G>T synonymous_variant 0.22
fbiB 3642710 c.1176G>T synonymous_variant 0.43
fbiB 3642759 p.Arg409Cys missense_variant 0.18
fbiB 3642768 c.1234C>T synonymous_variant 0.17
fbiB 3642786 p.Trp418Arg missense_variant 0.12
alr 3841180 p.Ala81Ser missense_variant 0.33
rpoA 3878307 c.201C>A synonymous_variant 0.22
rpoA 3878340 c.168C>A synonymous_variant 0.18
rpoA 3878630 c.-123G>C upstream_gene_variant 0.15
ddn 3986834 c.-10G>A upstream_gene_variant 0.2
ddn 3986992 p.Thr50Ile missense_variant 0.17
ddn 3987109 p.Tyr89Cys missense_variant 0.1
clpC1 4038227 c.2478G>A synonymous_variant 0.18
clpC1 4038585 p.Pro707Gln missense_variant 0.18
clpC1 4038602 c.2103G>A synonymous_variant 0.18
clpC1 4038734 p.Phe657Leu missense_variant 0.29
clpC1 4039024 p.Glu561Lys missense_variant 0.2
clpC1 4039174 p.Glu511Lys missense_variant 0.17
clpC1 4039190 c.1515C>A synonymous_variant 0.15
clpC1 4039304 p.Gln467His missense_variant 0.14
clpC1 4039364 c.1341C>T synonymous_variant 0.15
clpC1 4039419 p.Ala429Asp missense_variant 0.15
clpC1 4039816 p.Ala297Ser missense_variant 0.15
clpC1 4039829 p.Leu292Phe missense_variant 0.17
clpC1 4040346 p.Ala120Val missense_variant 0.15
clpC1 4040409 p.Gly99Val missense_variant 0.22
embC 4239926 p.Ala22Ser missense_variant 0.2
embC 4240163 p.Gly101Cys missense_variant 0.2
embC 4240285 c.423C>T synonymous_variant 0.4
embC 4240402 c.540C>A synonymous_variant 0.17
embC 4240547 p.Leu229Met missense_variant 0.14
embC 4240917 p.Ala352Val missense_variant 0.22
embC 4241300 p.Ala480Ser missense_variant 0.14
embC 4241660 p.Leu600Met missense_variant 0.17
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242735 p.Ile958Thr missense_variant 0.13
embA 4243054 c.-179G>A upstream_gene_variant 0.18
embC 4243136 p.Arg1092Cys missense_variant 0.15
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4243489 p.Gly86Val missense_variant 0.2
embA 4243989 p.Ala253Thr missense_variant 0.18
embA 4244990 c.1758G>T synonymous_variant 0.2
embA 4245116 c.1884C>A synonymous_variant 0.2
embA 4245919 p.Trp896Leu missense_variant 0.18
embB 4245935 c.-579G>T upstream_gene_variant 0.17
embA 4246104 p.Pro958Thr missense_variant 0.17
embB 4247621 p.Leu370Met missense_variant 0.17
embB 4247879 p.Val456Met missense_variant 0.2
embB 4247932 c.1419C>A synonymous_variant 0.25
embB 4249003 c.2490G>T synonymous_variant 0.15
embB 4249207 c.2694G>A synonymous_variant 0.22
aftB 4267003 c.1834C>A synonymous_variant 0.18
aftB 4267438 c.1399C>A synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269620 p.Val72Ile missense_variant 0.17
ethA 4326705 p.Pro257Thr missense_variant 0.15
ethA 4326807 p.Glu223Gln missense_variant 0.17
ethR 4327129 c.-420G>T upstream_gene_variant 0.17
ethR 4327393 c.-156G>A upstream_gene_variant 0.4
whiB6 4338208 p.Pro105Gln missense_variant 0.2
whiB6 4338417 c.105G>A synonymous_variant 0.25
whiB6 4338517 p.Arg2Leu missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407876 c.327C>A synonymous_variant 0.25
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4407976 p.Gly76Tyr missense_variant 0.18