TB-Profiler result

Run: ERR5864141
Summary

Run ID: ERR5864141

Sample name:

Date: 01-04-2023 23:08:51

Number of reads: 603855

Percentage reads mapped: 99.29

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
katG 2155801 p.Arg104Leu missense_variant 0.2 isoniazid
pncA 2289072 p.His57Arg 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 5189 c.-51C>T upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8333 p.Asn344Lys missense_variant 0.17
gyrA 8954 p.Gln551His missense_variant 0.15
gyrA 9245 c.1944C>A synonymous_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9684 p.Gly795* stop_gained 0.17
fgd1 491169 p.Phe129Leu missense_variant 0.27
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575329 c.-19C>A upstream_gene_variant 0.2
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576682 c.1335C>T synonymous_variant 0.2
ccsA 620396 p.Ser169Tyr missense_variant 0.4
ccsA 620625 p.Ile245Met missense_variant 1.0
ccsA 620824 p.Leu312Met missense_variant 0.22
rpoB 759614 c.-193C>A upstream_gene_variant 0.18
rpoB 759943 p.Gly46Val missense_variant 0.25
rpoB 760445 c.639C>A synonymous_variant 0.2
rpoB 760660 p.Ser285* stop_gained 0.2
rpoB 761567 p.Met587Ile missense_variant 0.25
rpoB 761642 c.1836G>T synonymous_variant 0.2
rpoB 761675 c.1869G>T synonymous_variant 0.18
rpoB 761819 c.2013G>T synonymous_variant 0.22
rpoB 761894 c.2088C>A synonymous_variant 0.22
rpoB 762440 p.Lys878Asn missense_variant 0.23
rpoB 762683 p.Glu959Asp missense_variant 0.25
rpoC 762983 c.-387C>A upstream_gene_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764515 p.Phe382Leu missense_variant 0.29
rpoC 765207 p.Ser613Tyr missense_variant 0.25
rpoC 765341 p.Pro658Ser missense_variant 0.25
rpoC 765395 p.Leu676Met missense_variant 0.18
rpoC 766364 p.Ala999Ser missense_variant 0.25
rpoC 766381 c.3012C>A synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776123 c.2358G>T synonymous_variant 0.22
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 776606 p.Gln625His missense_variant 0.17
mmpL5 777281 c.1200G>T synonymous_variant 0.2
mmpL5 777376 p.Glu369Lys missense_variant 0.2
mmpR5 778355 c.-635G>T upstream_gene_variant 0.23
mmpS5 778722 p.Gly62Ser missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781848 p.Ile97Val missense_variant 0.13
rpsL 781888 p.Arg110Leu missense_variant 0.17
rplC 800624 c.-185G>T upstream_gene_variant 0.19
rplC 801325 p.Asp173Tyr missense_variant 0.21
fbiC 1302956 p.Ser9Tyr missense_variant 0.22
fbiC 1303494 p.Leu188Phe missense_variant 0.22
fbiC 1304165 p.Gly412Val missense_variant 0.2
fbiC 1304772 c.1842C>T synonymous_variant 0.2
fbiC 1305070 p.Asp714Tyr missense_variant 0.25
fbiC 1305196 p.Ala756Ser missense_variant 0.18
fbiC 1305253 p.Ile775Val missense_variant 0.15
Rv1258c 1406420 p.Phe307Leu missense_variant 0.22
Rv1258c 1406432 p.Met303Ile missense_variant 0.2
Rv1258c 1406520 p.Gly274Val missense_variant 0.18
Rv1258c 1406619 p.Pro241Gln missense_variant 0.17
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1406802 p.Ala180Glu missense_variant 0.29
Rv1258c 1407216 p.Gly42Val missense_variant 0.17
Rv1258c 1407323 c.18C>T synonymous_variant 0.17
embR 1416452 p.Arg299Leu missense_variant 0.29
embR 1416532 c.816C>A synonymous_variant 0.2
embR 1416707 p.Ala214Asp missense_variant 0.15
embR 1416810 p.Ala180Ser missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472232 n.387G>T non_coding_transcript_exon_variant 0.33
rrs 1472424 n.579G>T non_coding_transcript_exon_variant 0.2
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.25
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.25
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.22
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.22
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.22
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.25
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.25
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.22
rrl 1473566 n.-92G>T upstream_gene_variant 0.22
rrl 1474865 n.1208C>A non_coding_transcript_exon_variant 0.29
rrl 1475360 n.1703G>T non_coding_transcript_exon_variant 0.5
rrl 1475761 n.2104C>A non_coding_transcript_exon_variant 0.2
rrl 1475837 n.2180C>A non_coding_transcript_exon_variant 0.29
rrl 1476146 n.2489G>T non_coding_transcript_exon_variant 0.22
rrl 1476626 n.2969G>T non_coding_transcript_exon_variant 0.25
inhA 1673442 c.-760G>T upstream_gene_variant 0.25
inhA 1674531 p.Asp110Glu missense_variant 0.18
rpsA 1834039 c.498C>A synonymous_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834315 c.774C>A synonymous_variant 0.18
rpsA 1834437 c.897delC frameshift_variant 0.22
rpsA 1834661 p.Asp374Tyr missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917975 c.36C>A synonymous_variant 0.18
tlyA 1918222 p.Gly95Trp missense_variant 0.2
tlyA 1918256 p.Ala106Asp missense_variant 0.17
ndh 2101761 p.Gln428Lys missense_variant 0.17
ndh 2102623 c.420C>A synonymous_variant 0.18
ndh 2102634 p.Gly137Cys missense_variant 0.2
ndh 2103108 c.-66G>T upstream_gene_variant 0.27
katG 2154545 p.Glu523* stop_gained 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155253 p.Glu287* stop_gained 0.23
katG 2155304 p.His270Asn missense_variant 0.23
katG 2155373 p.Asp247Tyr missense_variant 0.22
katG 2155938 p.Met58Ile missense_variant 0.23
katG 2156150 c.-39G>T upstream_gene_variant 0.22
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168223 p.Pro797Gln missense_variant 0.2
PPE35 2168685 c.1927delA frameshift_variant 0.15
PPE35 2170096 c.517C>A synonymous_variant 0.18
PPE35 2170407 p.Ala69Glu missense_variant 0.2
PPE35 2170592 c.21G>T synonymous_variant 0.2
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288771 c.471G>T synonymous_variant 0.18
pncA 2289664 c.-423G>T upstream_gene_variant 0.33
pncA 2289783 c.-542G>T upstream_gene_variant 0.31
pncA 2290140 c.-901_-900dupGC upstream_gene_variant 0.17
kasA 2518651 c.537C>A synonymous_variant 0.4
kasA 2518721 p.Glu203* stop_gained 0.29
kasA 2518750 p.Met212Ile missense_variant 0.22
kasA 2518855 c.741C>A synonymous_variant 0.29
kasA 2519136 p.Ser341Tyr missense_variant 0.27
eis 2715229 p.Ala35Asp missense_variant 0.16
folC 2746287 p.Asp438Tyr missense_variant 0.29
folC 2746336 c.1263C>A synonymous_variant 0.29
folC 2746565 p.Ala345Glu missense_variant 0.22
folC 2746621 c.978C>A synonymous_variant 0.33
folC 2747080 c.519C>A synonymous_variant 0.2
folC 2747456 p.Thr48Ile missense_variant 0.27
folC 2747537 p.Pro21Leu missense_variant 0.18
pepQ 2859333 p.Leu362Phe missense_variant 0.2
pepQ 2859596 p.Ala275Ser missense_variant 0.33
pepQ 2860489 c.-71G>T upstream_gene_variant 0.18
ribD 2986905 p.Leu23Ile missense_variant 0.18
ribD 2987133 p.Gly99Cys missense_variant 0.15
ribD 2987480 c.642G>T synonymous_variant 0.25
Rv2752c 3064533 c.1659G>T synonymous_variant 0.22
Rv2752c 3065615 p.Asp193Tyr missense_variant 0.2
Rv2752c 3065987 p.Asp69Tyr missense_variant 0.18
Rv2752c 3066198 c.-7C>A upstream_gene_variant 0.22
Rv2752c 3067024 c.-833C>T upstream_gene_variant 0.18
thyX 3067710 p.Ser79* stop_gained 0.29
thyX 3067754 c.192C>A synonymous_variant 0.33
thyA 3074272 p.Ser67Tyr missense_variant 0.18
ald 3086731 c.-89A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087503 c.684C>A synonymous_variant 0.18
ald 3087874 p.Ser352Tyr missense_variant 0.2
fbiD 3339156 c.39C>A synonymous_variant 0.2
fbiD 3339539 p.Ala141Asp missense_variant 0.18
Rv3083 3448518 p.Phe5Leu missense_variant 0.22
Rv3083 3448557 c.54G>T synonymous_variant 0.25
Rv3083 3448585 p.Pro28Thr missense_variant 0.29
Rv3083 3448686 c.183C>A synonymous_variant 0.18
Rv3083 3449183 p.Ser227Tyr missense_variant 0.18
Rv3083 3449352 p.Met283Ile missense_variant 0.3
Rv3083 3449768 p.Thr422Lys missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568624 p.Pro19Gln missense_variant 0.18
whiB7 3568777 c.-98C>A upstream_gene_variant 0.18
Rv3236c 3611979 p.Ala380Ser missense_variant 0.22
Rv3236c 3612406 p.His237Gln missense_variant 0.33
Rv3236c 3612705 p.Glu138* stop_gained 0.29
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640615 p.Leu25Met missense_variant 0.15
fbiA 3640627 p.Ala29Ser missense_variant 0.18
fbiA 3641150 p.Leu203Pro missense_variant 0.22
fbiA 3641384 p.Ala281Asp missense_variant 0.17
fbiB 3641702 p.Cys56* stop_gained 0.2
fbiB 3641765 c.231G>T synonymous_variant 0.29
fbiB 3642425 p.Phe297Leu missense_variant 0.24
rpoA 3877545 c.963G>T synonymous_variant 0.23
rpoA 3878138 p.His124Asn missense_variant 0.22
rpoA 3878490 c.18C>A synonymous_variant 0.22
ddn 3986924 p.Trp27Cys missense_variant 0.2
clpC1 4038216 p.Pro830Gln missense_variant 0.33
clpC1 4038677 c.2028G>T synonymous_variant 0.25
clpC1 4039739 c.966C>A synonymous_variant 0.17
clpC1 4040291 c.414G>T synonymous_variant 0.23
clpC1 4040333 c.372G>T synonymous_variant 0.17
clpC1 4040444 c.261C>A synonymous_variant 0.18
panD 4044048 p.Leu78Phe missense_variant 0.3
panD 4044376 c.-95C>A upstream_gene_variant 0.22
panD 4044434 c.-153G>T upstream_gene_variant 0.22
embC 4240585 c.723C>A synonymous_variant 0.29
embC 4240635 p.Arg258Leu missense_variant 0.4
embC 4241029 p.Trp389Cys missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242812 p.Asp984Tyr missense_variant 0.2
embA 4243346 c.114A>G synonymous_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244756 p.Glu508Asp missense_variant 0.33
embA 4244855 c.1623G>T synonymous_variant 0.29
embA 4246100 p.Phe956Leu missense_variant 0.22
embA 4246204 p.Arg991Leu missense_variant 0.22
embB 4246223 c.-291C>A upstream_gene_variant 0.33
embB 4246714 c.201G>T synonymous_variant 0.22
embB 4247336 p.Thr275Ala missense_variant 0.12
embB 4247546 p.Asp345Tyr missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4268019 p.Ser273* stop_gained 0.27
aftB 4268139 p.Gly233Val missense_variant 0.2
aftB 4269237 c.-401C>A upstream_gene_variant 0.22
aftB 4269384 c.-548C>A upstream_gene_variant 0.25
ethA 4326496 c.978G>T synonymous_variant 0.22
ethA 4326508 c.966G>T synonymous_variant 0.18
ethR 4326622 c.-927C>A upstream_gene_variant 0.22
ethA 4327075 p.Phe133Leu missense_variant 0.29
whiB6 4338316 p.Ser69Tyr missense_variant 0.17
whiB6 4338371 p.Thr51Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338673 c.-152G>T upstream_gene_variant 0.2
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0