TB-Profiler result

Run: ERR4817987
Summary

Run ID: ERR4817987

Sample name:

Date: 01-04-2023 15:18:10

Number of reads: 786622

Percentage reads mapped: 80.79

Strain: lineage4.7

Drug-resistance: Other

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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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.7 Euro-American (mainly T) T1;T5 None 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 1472733 n.888G>A non_coding_transcript_exon_variant 1.0 streptomycin
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 5771 p.Ala178Thr missense_variant 0.29
gyrB 5779 c.540C>T synonymous_variant 0.29
gyrB 5814 p.Arg192His missense_variant 0.18
gyrB 6522 p.Arg428Gln missense_variant 0.17
gyrB 6913 p.Asn558Lys missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7720 p.Glu140Val missense_variant 0.18
gyrA 7935 p.Glu212Lys missense_variant 0.17
gyrA 8409 p.Leu370Ile missense_variant 0.15
gyrA 8539 p.Thr413Ile missense_variant 0.2
gyrA 8819 c.1518C>T synonymous_variant 0.5
gyrA 9464 c.2163C>T synonymous_variant 0.18
gyrA 9637 p.Ser779Phe missense_variant 0.15
gyrA 9690 p.Gln797Lys missense_variant 0.13
mshA 575248 c.-100C>T upstream_gene_variant 0.12
mshA 575389 c.42C>A synonymous_variant 0.33
mshA 575846 p.Asp167Tyr missense_variant 0.18
mshA 576255 p.Gly303Asp missense_variant 0.29
ccsA 619837 c.-54G>T upstream_gene_variant 0.17
ccsA 620298 c.408G>A synonymous_variant 0.18
ccsA 620406 c.516G>T synonymous_variant 0.18
ccsA 620679 c.791delA frameshift_variant 0.25
ccsA 620833 p.Val315Ile missense_variant 0.13
rpoB 760301 c.496delG frameshift_variant 0.17
rpoB 760545 p.Gly247Arg missense_variant 0.12
rpoB 760767 p.Pro321Ser missense_variant 0.17
rpoB 760995 p.Arg397Trp missense_variant 0.29
rpoB 761204 c.1398C>A synonymous_variant 0.22
rpoB 761647 p.Arg614His missense_variant 0.12
rpoB 761952 p.Ala716Ser missense_variant 0.12
rpoB 761996 c.2190C>A synonymous_variant 0.18
rpoC 762536 c.-834T>C upstream_gene_variant 0.17
rpoC 763575 p.Arg69His missense_variant 0.33
rpoC 763647 p.Gly93Val missense_variant 0.2
rpoC 763730 c.365delC frameshift_variant 0.14
rpoC 763791 p.Glu141Val missense_variant 0.17
rpoC 764246 p.Leu293Ile missense_variant 0.13
rpoC 764609 c.1240C>A synonymous_variant 0.15
rpoC 765170 p.Pro601Thr missense_variant 0.29
rpoC 765290 p.Arg641Trp missense_variant 0.29
rpoC 765971 p.Ala868Thr missense_variant 0.13
rpoC 766433 p.Glu1022* stop_gained 0.14
rpoC 766460 p.Val1031Met missense_variant 0.22
rpoC 766968 p.Pro1200His missense_variant 0.29
rpoC 766996 c.3627C>A synonymous_variant 0.2
rpoC 767146 c.3777G>A synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775964 c.2517G>A synonymous_variant 0.14
mmpL5 776531 c.1950G>T synonymous_variant 0.22
mmpL5 776889 p.Ser531Tyr missense_variant 0.18
mmpL5 777119 p.His454Gln missense_variant 0.18
mmpL5 777122 c.1359C>T synonymous_variant 0.18
mmpL5 777128 c.1353A>G synonymous_variant 0.18
mmpR5 778202 c.-788G>A upstream_gene_variant 0.22
mmpL5 778256 p.Met75Ile missense_variant 0.12
mmpS5 779647 c.-742G>T upstream_gene_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>T upstream_gene_variant 0.15
rplC 801309 c.501C>T synonymous_variant 0.22
fbiC 1303725 c.795G>A synonymous_variant 0.18
fbiC 1303911 c.981G>A synonymous_variant 0.25
fbiC 1304333 p.Ser468Ile missense_variant 0.12
fbiC 1304706 p.His592Gln missense_variant 0.25
fbiC 1304758 p.Pro610Thr missense_variant 0.14
fbiC 1304806 p.Pro626Thr missense_variant 0.33
fbiC 1305022 p.His698Asp missense_variant 0.22
fbiC 1305417 c.2487C>A synonymous_variant 0.13
fbiC 1305469 p.Arg847Ser missense_variant 0.18
fbiC 1305491 p.Leu854His missense_variant 0.18
Rv1258c 1406608 p.Val245Met missense_variant 0.17
Rv1258c 1406711 c.630C>T synonymous_variant 0.2
Rv1258c 1406981 c.360C>A synonymous_variant 0.12
Rv1258c 1407440 c.-100C>A upstream_gene_variant 0.17
embR 1416222 p.Phe376Leu missense_variant 0.14
embR 1416232 p.Cys372Gly missense_variant 0.15
embR 1416259 c.1089G>C synonymous_variant 0.2
embR 1416422 p.Arg309Leu missense_variant 0.17
embR 1416606 p.Arg248Cys missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 1.0
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 1.0
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 1.0
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 1.0
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 1.0
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 1.0
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 1.0
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 1.0
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 1.0
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 1.0
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 1.0
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 1.0
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 1.0
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 1.0
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 1.0
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 1.0
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 1.0
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 1.0
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 1.0
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 1.0
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 1.0
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 1.0
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 1.0
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 1.0
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 1.0
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 1.0
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 1.0
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 1.0
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 1.0
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 1.0
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 1.0
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 1.0
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 1.0
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 1.0
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 1.0
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.67
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.67
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 1.0
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 1.0
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.96
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.97
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.97
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.97
rrs 1473248 n.1403G>A non_coding_transcript_exon_variant 0.8
rrs 1473249 n.1404T>C non_coding_transcript_exon_variant 0.8
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.8
rrs 1473255 n.1410A>G non_coding_transcript_exon_variant 0.8
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 1.0
rrs 1473260 n.1415G>T non_coding_transcript_exon_variant 1.0
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 1.0
rrs 1473301 n.1456T>G non_coding_transcript_exon_variant 1.0
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 1.0
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 1.0
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 1.0
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 1.0
rrl 1474252 n.595T>A non_coding_transcript_exon_variant 1.0
rrl 1474275 n.618T>C non_coding_transcript_exon_variant 1.0
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 1.0
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>G non_coding_transcript_exon_variant 1.0
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 1.0
rrl 1476227 n.2570C>T non_coding_transcript_exon_variant 1.0
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 1.0
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 1.0
rrl 1476257 n.2600G>C non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 1.0
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.5
fabG1 1673189 c.-251A>G upstream_gene_variant 0.15
fabG1 1673222 c.-218G>A upstream_gene_variant 0.18
inhA 1673409 c.-793C>T upstream_gene_variant 0.17
inhA 1673610 c.-592C>T upstream_gene_variant 0.2
inhA 1674358 p.Arg53Gly missense_variant 0.29
inhA 1674574 p.Tyr125His missense_variant 0.12
rpsA 1834607 p.Arg356Gly missense_variant 0.33
rpsA 1834828 c.1287C>T synonymous_variant 0.5
rpsA 1834872 p.Gly444Val missense_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918399 p.Asp154Asn missense_variant 0.12
tlyA 1918434 c.495C>A synonymous_variant 0.12
tlyA 1918662 c.723G>T synonymous_variant 0.12
ndh 2101861 c.1182G>T synonymous_variant 0.22
ndh 2102148 p.Arg299Trp missense_variant 0.2
ndh 2102401 c.642T>C synonymous_variant 0.1
ndh 2102486 p.Ala186Val missense_variant 0.25
ndh 2102561 p.Ser161Tyr missense_variant 0.22
ndh 2102725 p.His106Gln missense_variant 0.15
ndh 2103136 c.-94C>G upstream_gene_variant 0.14
katG 2154294 c.1818C>A synonymous_variant 0.17
katG 2154317 p.Gly599Arg missense_variant 0.22
katG 2154521 p.Ala531Ser missense_variant 0.18
katG 2154652 p.Asp487Gly missense_variant 0.17
katG 2154702 c.1410A>C synonymous_variant 0.15
katG 2156553 c.-442G>A upstream_gene_variant 0.17
PPE35 2168868 p.Pro582Arg missense_variant 0.12
PPE35 2169099 p.Gly505Glu missense_variant 0.17
PPE35 2169580 p.Gly345Cys missense_variant 0.33
PPE35 2170403 c.210C>G synonymous_variant 0.12
PPE35 2170406 c.207A>G synonymous_variant 0.12
Rv1979c 2221767 p.His466Gln missense_variant 0.11
Rv1979c 2222641 p.Ser175Leu missense_variant 0.17
Rv1979c 2223067 p.Phe33Ser missense_variant 0.18
Rv1979c 2223079 p.Gly29Val missense_variant 0.2
Rv1979c 2223092 p.Asn25Asp missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223314 c.-150C>A upstream_gene_variant 0.12
pncA 2288759 c.483G>T synonymous_variant 0.15
pncA 2289018 p.Gly75Asp missense_variant 0.17
pncA 2290131 c.-890G>A upstream_gene_variant 0.14
kasA 2518169 p.Val19Ile missense_variant 0.25
kasA 2518417 c.303G>A synonymous_variant 0.14
kasA 2518804 c.690C>T synonymous_variant 0.14
kasA 2519128 c.1014G>A synonymous_variant 0.22
kasA 2519131 c.1017G>A synonymous_variant 0.22
kasA 2519335 p.His407Gln missense_variant 0.14
eis 2714569 p.Ala255Val missense_variant 0.15
eis 2715225 p.Trp36* stop_gained 0.15
ahpC 2726192 c.-1C>T upstream_gene_variant 0.25
ahpC 2726459 p.Ser89Arg missense_variant 0.12
ahpC 2726528 c.336C>A synonymous_variant 0.12
folC 2746229 p.Ala457Val missense_variant 0.17
folC 2746295 p.Asn435Ile missense_variant 0.12
folC 2746648 c.951G>A synonymous_variant 0.18
folC 2746660 c.938delT frameshift_variant 0.18
folC 2746831 c.768G>A synonymous_variant 0.25
folC 2746859 p.Ala247Asp missense_variant 0.18
folC 2746873 p.Met242Ile missense_variant 0.2
folC 2747064 p.Gly179Arg missense_variant 0.2
folC 2747080 c.519C>A synonymous_variant 0.12
folC 2747433 c.166C>T synonymous_variant 0.12
pepQ 2859529 p.Gly297Asp missense_variant 0.18
ribD 2986710 c.-129C>A upstream_gene_variant 0.25
ribD 2986810 c.-29C>T upstream_gene_variant 0.33
Rv2752c 3065175 c.1017G>T synonymous_variant 0.13
Rv2752c 3065506 p.Ala229Val missense_variant 0.17
Rv2752c 3065526 c.666G>A synonymous_variant 0.17
Rv2752c 3065805 c.387C>T synonymous_variant 0.14
Rv2752c 3066006 c.186G>A synonymous_variant 0.15
Rv2752c 3066035 p.Asp53Asn missense_variant 0.17
Rv2752c 3066171 c.21G>A synonymous_variant 0.22
Rv2752c 3066241 c.-50C>T upstream_gene_variant 0.29
thyX 3067223 c.723G>A synonymous_variant 0.17
thyX 3067278 p.Ala223Asp missense_variant 0.14
thyX 3067456 p.Arg164Cys missense_variant 0.15
thyX 3068092 c.-147C>A upstream_gene_variant 0.12
thyA 3073901 p.Gln191Lys missense_variant 0.12
thyA 3073972 p.Ser167Ile missense_variant 0.18
thyA 3074445 c.27C>T synonymous_variant 0.29
thyA 3074570 c.-99C>A upstream_gene_variant 0.22
ald 3086981 c.162C>T synonymous_variant 0.17
ald 3087929 c.1110G>T synonymous_variant 0.2
fbiD 3339672 c.555G>T synonymous_variant 0.12
Rv3083 3448331 c.-173G>A upstream_gene_variant 0.12
Rv3083 3449080 p.Val193Ile missense_variant 0.25
Rv3083 3449319 c.816G>A synonymous_variant 0.2
fprA 3473874 c.-133C>T upstream_gene_variant 0.14
fprA 3474143 p.Trp46Tyr missense_variant 0.2
fprA 3474163 p.Val53Phe missense_variant 0.22
fprA 3474715 p.Asp237Asn missense_variant 0.13
fprA 3475055 c.1050delC frameshift_variant 0.2
whiB7 3568845 c.-166G>A upstream_gene_variant 0.18
whiB7 3568871 c.-192C>A upstream_gene_variant 0.14
Rv3236c 3612875 p.Glu81Gly missense_variant 0.25
Rv3236c 3612898 c.219G>T synonymous_variant 0.2
fbiA 3640533 c.-10G>T upstream_gene_variant 0.14
fbiA 3641377 p.Arg279Trp missense_variant 0.25
fbiB 3641999 c.465C>T synonymous_variant 0.25
fbiB 3642389 c.855C>T synonymous_variant 0.13
fbiB 3642432 p.Leu300Met missense_variant 0.12
alr 3841288 p.Ile45Phe missense_variant 0.15
alr 3841291 p.Ala44Ser missense_variant 0.15
rpoA 3877794 c.714G>A synonymous_variant 0.2
clpC1 4038454 c.2251C>T synonymous_variant 0.22
clpC1 4039275 p.Ala477Glu missense_variant 0.15
clpC1 4039691 c.1014G>C synonymous_variant 0.29
clpC1 4039714 p.Tyr331His missense_variant 0.2
clpC1 4039804 p.Ala301Ser missense_variant 0.22
panD 4043930 p.Gly118Cys missense_variant 0.12
embC 4240651 c.792delC frameshift_variant 0.17
embC 4241210 p.Leu450Met missense_variant 0.22
embC 4241426 p.Leu522Met missense_variant 0.2
embC 4241961 p.Leu700Gln missense_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243553 c.321C>T synonymous_variant 0.2
embA 4243625 c.393C>A synonymous_variant 0.13
embA 4244284 p.Pro351Arg missense_variant 0.25
embA 4244779 p.Ser516Tyr missense_variant 0.2
embA 4245456 p.Glu742Lys missense_variant 0.25
embA 4245528 p.Gly766Cys missense_variant 0.12
embA 4245804 p.Gln858* stop_gained 0.17
embA 4245982 p.Gly917Val missense_variant 0.15
embB 4246679 p.Leu56Ile missense_variant 0.2
embB 4246979 p.Gly156Ser missense_variant 0.12
embB 4247031 p.Arg173His missense_variant 0.14
embB 4247818 c.1305C>A synonymous_variant 0.13
embB 4248430 c.1917T>C synonymous_variant 0.15
embB 4248728 p.Asn739Asp missense_variant 0.33
embB 4249047 p.Ala845Gly missense_variant 0.17
embB 4249153 c.2640G>A synonymous_variant 0.22
embB 4249732 c.3219C>G synonymous_variant 1.0
aftB 4267076 p.Phe587Leu missense_variant 0.14
aftB 4267916 c.921T>C synonymous_variant 0.25
aftB 4268203 c.634C>T synonymous_variant 0.2
aftB 4268266 p.Leu191Met missense_variant 0.2
aftB 4268441 c.396C>A synonymous_variant 0.17
aftB 4268774 p.Ser21Arg missense_variant 0.18
aftB 4268831 c.6C>A synonymous_variant 0.12
ubiA 4269268 p.Ala189Asp missense_variant 0.2
ubiA 4269449 p.Val129Ile missense_variant 0.17
ubiA 4269814 p.Thr7Ser missense_variant 0.17
ethR 4326904 c.-645G>C upstream_gene_variant 0.2
ethA 4327016 p.Gly153Asp missense_variant 0.15
ethA 4327596 c.-123G>C upstream_gene_variant 0.2
whiB6 4338247 p.Leu92* stop_gained 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407627 c.576C>T synonymous_variant 0.13
gid 4407959 p.Ala82Thr missense_variant 0.14
gid 4408012 p.Arg64Gln missense_variant 0.29
gid 4408375 c.-173G>A upstream_gene_variant 0.18