TB-Profiler result

Run: ERR2245360
Summary

Run ID: ERR2245360

Sample name:

Date: 31-03-2023 17:39:32

Number of reads: 1690755

Percentage reads mapped: 98.87

Strain: lineage3.1.1

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
lineage3 East-African-Indian CAS RD750 1.0
lineage3.1.1 East-African-Indian CAS1-Kili RD750 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 5443 c.204G>T synonymous_variant 0.18
gyrB 5699 p.Glu154* stop_gained 0.27
gyrB 5747 p.Thr170Ala missense_variant 0.22
gyrB 6350 p.Thr371Ala missense_variant 0.18
gyrB 6393 p.Gln385Leu missense_variant 0.18
gyrB 6437 p.Pro400Thr missense_variant 0.3
gyrA 6739 c.-563C>A upstream_gene_variant 0.22
gyrB 6993 p.Arg585His missense_variant 0.17
gyrA 7147 c.-155G>T upstream_gene_variant 0.4
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7503 p.Arg68Cys missense_variant 0.33
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8917 p.Arg539Leu missense_variant 0.18
gyrA 8925 p.Lys542Glu missense_variant 0.17
gyrA 8978 c.1677C>T synonymous_variant 0.17
gyrA 9003 p.Leu568Val missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9780 p.Ala827Thr missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
fgd1 491757 p.Gln325His missense_variant 0.25
mshA 575920 c.573C>A synonymous_variant 0.5
mshA 576108 p.Ala254Gly missense_variant 0.38
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 760078 p.Glu91Gly missense_variant 0.29
rpoB 760290 p.Ile162Phe missense_variant 0.33
rpoB 760481 c.675G>A synonymous_variant 0.29
rpoB 760638 p.Gly278Cys missense_variant 0.22
rpoB 760658 p.Glu284Asp missense_variant 0.22
rpoB 760749 p.Gly315Trp missense_variant 0.2
rpoB 761267 p.Asn487Lys missense_variant 0.33
rpoB 761961 p.Pro719Thr missense_variant 0.22
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763117 p.Glu1104Ala missense_variant 0.4
rpoB 763263 p.Ala1153Thr missense_variant 0.14
rpoC 763444 c.75T>C synonymous_variant 0.2
rpoC 763865 p.Arg166Cys missense_variant 0.29
rpoC 764234 p.Lys289Gln missense_variant 0.22
rpoC 764912 p.Met515Val missense_variant 0.17
rpoC 765237 p.Asp623Ala missense_variant 0.5
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776073 p.Val803Gly missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpR5 778106 c.-884G>T upstream_gene_variant 0.29
mmpS5 778799 p.Gly36Val missense_variant 0.14
mmpR5 779082 p.Ser31Arg missense_variant 0.17
mmpR5 779322 p.Met111Ile missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781688 p.Lys43Asn missense_variant 0.13
fbiC 1304645 p.Gly572Val missense_variant 0.33
fbiC 1304914 p.Asp662Tyr missense_variant 0.22
fbiC 1305183 p.Leu751Phe missense_variant 0.18
fbiC 1305286 p.Thr786Ser missense_variant 0.4
Rv1258c 1406504 c.837C>T synonymous_variant 0.4
Rv1258c 1406873 c.468C>T synonymous_variant 0.29
Rv1258c 1407068 c.273G>T synonymous_variant 0.25
embR 1416459 p.Ser297Thr missense_variant 0.5
embR 1416837 p.Val171Ile missense_variant 0.4
embR 1417194 p.Val52Ile missense_variant 0.25
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472717 n.872C>A non_coding_transcript_exon_variant 0.5
rrs 1473314 n.1469A>G non_coding_transcript_exon_variant 0.14
rrl 1475513 n.1856T>C non_coding_transcript_exon_variant 0.22
rrl 1476336 n.2679C>A non_coding_transcript_exon_variant 0.33
rrl 1476558 n.2901G>T non_coding_transcript_exon_variant 0.33
inhA 1673925 c.-277C>A upstream_gene_variant 1.0
rpsA 1833969 p.Gly143Val missense_variant 0.25
rpsA 1834335 c.795delC frameshift_variant 0.22
rpsA 1834962 p.Arg474Gln missense_variant 0.4
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917982 p.Gly15Cys missense_variant 0.29
tlyA 1918176 c.237C>A synonymous_variant 0.4
katG 2154177 c.1935G>A synonymous_variant 0.25
katG 2154548 p.Glu522* stop_gained 0.25
katG 2154974 p.Thr380Ser missense_variant 0.33
katG 2155302 c.810C>T synonymous_variant 0.4
katG 2156306 c.-195C>A upstream_gene_variant 0.18
katG 2156335 c.-224C>A upstream_gene_variant 0.25
katG 2156454 c.-343G>T upstream_gene_variant 0.17
katG 2156551 c.-440C>A upstream_gene_variant 0.33
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168018 c.2595C>A synonymous_variant 0.29
PPE35 2168876 p.Phe579Leu missense_variant 0.29
PPE35 2168882 c.1731T>A synonymous_variant 0.25
PPE35 2169498 p.Phe372Ser missense_variant 0.12
PPE35 2169902 p.Leu237Phe missense_variant 0.17
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
PPE35 2170059 p.Val185Gly missense_variant 0.18
PPE35 2170141 p.Ala158Ser missense_variant 0.5
PPE35 2170439 p.Gln58His missense_variant 0.4
PPE35 2170461 p.Gly51Glu missense_variant 1.0
Rv1979c 2222032 p.Ala378Val missense_variant 0.25
Rv1979c 2222226 p.Phe313Leu missense_variant 0.33
Rv1979c 2222423 p.Pro248Ala missense_variant 0.29
Rv1979c 2222918 p.Thr83Pro missense_variant 0.18
Rv1979c 2223195 c.-31A>T upstream_gene_variant 0.22
Rv1979c 2223291 c.-127G>T upstream_gene_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289059 c.183A>C synonymous_variant 0.25
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2289933 c.-692G>T upstream_gene_variant 0.25
kasA 2518288 c.174C>A synonymous_variant 0.17
eis 2714568 c.765C>A synonymous_variant 0.17
eis 2715570 c.-238C>T upstream_gene_variant 0.33
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746302 p.Ala433Ser missense_variant 0.33
folC 2746439 p.Val387Ala missense_variant 0.4
folC 2747081 p.Val173Gly missense_variant 0.29
folC 2747132 p.Thr156Ile missense_variant 0.22
pepQ 2859912 p.Glu169Asp missense_variant 0.25
pepQ 2860159 p.Ala87Val missense_variant 0.33
pepQ 2860586 c.-168C>A upstream_gene_variant 0.5
ribD 2987412 p.Thr192Ala missense_variant 0.4
Rv2752c 3064566 c.1626G>C synonymous_variant 0.33
Rv2752c 3065800 p.Gly131Ala missense_variant 0.18
thyX 3067479 p.Asp156Ala missense_variant 0.4
thyA 3074506 c.-35C>A upstream_gene_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087456 p.Gly213Cys missense_variant 0.29
fbiD 3339605 p.Gly163Val missense_variant 0.29
fbiD 3339727 p.Gly204Trp missense_variant 0.4
Rv3083 3448668 c.165G>T synonymous_variant 0.5
Rv3083 3448948 p.Tyr149Asn missense_variant 0.4
Rv3083 3449171 p.Val223Gly missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474445 p.Gly147Cys missense_variant 0.18
fprA 3475275 p.Trp423Cys missense_variant 0.4
fbiA 3641015 p.Asp158Ala missense_variant 0.25
fbiB 3641866 p.Ser111Tyr missense_variant 0.4
rpoA 3877495 p.Glu338Ala missense_variant 0.33
rpoA 3878144 p.Gly122Cys missense_variant 0.29
rpoA 3878164 p.Gly115Val missense_variant 0.2
rpoA 3878490 c.18C>G synonymous_variant 0.5
clpC1 4038538 p.Thr723Pro missense_variant 0.4
clpC1 4038893 c.1812C>T synonymous_variant 0.29
clpC1 4039031 c.1674T>C synonymous_variant 0.17
clpC1 4039045 p.Pro554Thr missense_variant 0.18
clpC1 4039109 c.1596C>A synonymous_variant 0.2
clpC1 4039730 c.975C>G synonymous_variant 0.29
clpC1 4039892 p.Lys271Asn missense_variant 0.29
clpC1 4040344 p.Ala121Thr missense_variant 0.4
clpC1 4040500 p.Gln69Lys missense_variant 0.18
embC 4240084 c.222G>T synonymous_variant 0.25
embC 4240172 p.Val104Met missense_variant 1.0
embC 4240290 p.Pro143Gln missense_variant 0.25
embC 4241491 c.1629G>T synonymous_variant 0.29
embC 4241562 p.Arg567His missense_variant 1.0
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243899 p.Ala223Ser missense_variant 0.33
embA 4244821 p.Gly530Val missense_variant 0.33
embA 4245245 c.2013C>T synonymous_variant 0.2
embB 4245716 c.-798G>T upstream_gene_variant 0.5
embA 4245723 p.Gly831Arg missense_variant 0.5
embB 4247164 c.651G>T synonymous_variant 0.4
embB 4247300 p.Gly263Cys missense_variant 0.18
embB 4247636 p.Pro375Ser missense_variant 0.2
embB 4248441 p.Thr643Asn missense_variant 0.25
embB 4248499 p.Lys662Asn missense_variant 0.14
embB 4249052 p.Thr847Pro missense_variant 0.4
aftB 4267318 p.Gln507Lys missense_variant 0.33
aftB 4267422 p.Thr472Ile missense_variant 0.33
aftB 4268619 p.Val73Gly missense_variant 0.4
aftB 4269222 c.-386T>G upstream_gene_variant 0.22
ethA 4326141 p.Glu445* stop_gained 0.2
ethA 4326204 p.Ser424Ala missense_variant 0.18
ethA 4326223 c.1251G>T synonymous_variant 0.22
ethA 4326979 p.Gln165His missense_variant 0.29
ethA 4327006 p.Asp156Glu missense_variant 0.22
ethR 4327045 c.-504G>A upstream_gene_variant 0.29
ethA 4327863 c.-390G>A upstream_gene_variant 0.33
ethR 4328055 p.His169Gln missense_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0