TB-Profiler result

Run: SRR1175304
Summary

Run ID: SRR1175304

Sample name:

Date: 03-04-2023 03:38:49

Number of reads: 795680

Percentage reads mapped: 12.1

Strain: lineage4.3.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 761161 p.Leu452Pro missense_variant 0.89 rifampicin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.92 streptomycin
fabG1 1673432 c.-8T>A upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288785 c.456dupC frameshift_variant 1.0 pyrazinamide, pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327484 c.-11A>G upstream_gene_variant 1.0 ethionamide
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8457 p.Glu386* stop_gained 0.14
gyrA 8918 c.1617C>A synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490926 c.144C>T synonymous_variant 0.22
mshA 575914 c.567C>T synonymous_variant 0.29
mshA 575959 p.Gln204His missense_variant 0.2
mshA 576461 p.Ala372Thr missense_variant 0.33
ccsA 619740 c.-151C>T upstream_gene_variant 0.25
ccsA 620554 p.Ala222Ser missense_variant 0.15
rpoB 760334 c.528G>T synonymous_variant 0.13
rpoB 760658 p.Glu284Asp missense_variant 0.22
rpoB 761239 p.Cys478Phe missense_variant 0.18
rpoC 762899 c.-471G>C upstream_gene_variant 0.13
rpoB 763086 p.Val1094Phe missense_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 0.95
rpoC 765862 p.Phe831Leu missense_variant 0.13
rpoC 765890 p.Arg841Gly missense_variant 0.11
rpoC 766014 c.2647delG frameshift_variant 0.22
rpoC 766490 p.Arg1041Ser missense_variant 0.14
rpoC 766594 c.3225G>T synonymous_variant 0.25
rpoC 766714 c.3345G>T synonymous_variant 0.29
rpoC 767108 p.Gly1247Cys missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777035 p.Gln482His missense_variant 0.18
mmpR5 779254 p.Arg89Trp missense_variant 0.17
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781657 p.Val33Glu missense_variant 0.12
rplC 800867 p.Ser20Ile missense_variant 0.15
rplC 801049 p.Leu81Met missense_variant 0.14
fbiC 1303120 p.Arg64Trp missense_variant 0.29
fbiC 1303872 p.Tyr314* stop_gained 0.22
fbiC 1304323 p.Asp465Tyr missense_variant 0.17
fbiC 1304611 p.Gly561Ser missense_variant 0.2
fbiC 1305442 p.Glu838Lys missense_variant 0.15
Rv1258c 1406716 p.Val209Leu missense_variant 0.12
Rv1258c 1406732 c.609G>T synonymous_variant 0.12
Rv1258c 1406988 p.Pro118Gln missense_variant 0.22
Rv1258c 1407416 c.-76C>A upstream_gene_variant 0.18
embR 1416621 p.Pro243Thr missense_variant 0.17
embR 1417138 c.210G>T synonymous_variant 0.18
atpE 1461095 p.Met17Ile missense_variant 0.22
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.2
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.29
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.31
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.31
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.31
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.35
rrs 1472128 n.283G>A non_coding_transcript_exon_variant 0.35
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.35
rrs 1472130 n.285G>A non_coding_transcript_exon_variant 0.35
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.38
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.38
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.38
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.4
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.17
rrs 1472498 n.653C>A non_coding_transcript_exon_variant 0.28
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.75
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.78
rrs 1472518 n.673G>T non_coding_transcript_exon_variant 0.79
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.86
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.88
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.88
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.88
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.9
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.91
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.92
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.93
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.93
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.93
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.91
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.82
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.82
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.82
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.74
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.64
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.7
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.7
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.7
rrs 1472687 n.842_843insC non_coding_transcript_exon_variant 0.7
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.73
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.81
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.88
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.89
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.91
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.91
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.87
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.83
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.77
rrs 1472824 n.979T>A non_coding_transcript_exon_variant 0.5
rrs 1472827 n.982G>T non_coding_transcript_exon_variant 0.25
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.31
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.27
rrs 1472992 n.1147A>G non_coding_transcript_exon_variant 0.28
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.26
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.38
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.24
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.32
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.2
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.18
rrs 1473130 n.1285G>A non_coding_transcript_exon_variant 0.37
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.39
rrs 1473147 n.1302G>T non_coding_transcript_exon_variant 0.37
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.32
rrs 1473150 n.1305T>G non_coding_transcript_exon_variant 0.34
rrs 1473161 n.1316A>C non_coding_transcript_exon_variant 0.37
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.36
rrs 1473164 n.1319C>A non_coding_transcript_exon_variant 0.36
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.44
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.39
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.37
rrs 1473199 n.1356delA non_coding_transcript_exon_variant 0.41
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.38
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.16
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14
rrl 1474516 n.859C>T non_coding_transcript_exon_variant 0.17
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.14
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.15
rrl 1474674 n.1018delC non_coding_transcript_exon_variant 0.18
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.19
rrl 1474709 n.1052G>A non_coding_transcript_exon_variant 0.12
rrl 1474722 n.1065T>C non_coding_transcript_exon_variant 0.11
rrl 1474734 n.1077G>T non_coding_transcript_exon_variant 0.16
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.14
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.23
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.13
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.13
rrl 1474839 n.1182C>T non_coding_transcript_exon_variant 0.2
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.2
rrl 1474848 n.1191G>A non_coding_transcript_exon_variant 0.21
rrl 1474862 n.1205C>T non_coding_transcript_exon_variant 0.23
rrl 1474892 n.1235G>A non_coding_transcript_exon_variant 0.2
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.21
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.11
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.12
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.22
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.4
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.45
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.46
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.51
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.51
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.42
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.4
rrl 1475874 n.2217C>T non_coding_transcript_exon_variant 0.29
rrl 1475877 n.2220C>T non_coding_transcript_exon_variant 0.2
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.31
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.29
rrl 1475896 n.2239A>G non_coding_transcript_exon_variant 0.19
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.19
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.19
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.21
rrl 1475906 n.2249C>T non_coding_transcript_exon_variant 0.21
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.21
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.17
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.17
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.16
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 1.0
rrl 1476250 n.2593C>G non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.15
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.15
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.32
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.71
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.75
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.82
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.83
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.84
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.84
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.86
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.86
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.9
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.92
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.92
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.81
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.38
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.12
rrl 1476585 n.2928A>G non_coding_transcript_exon_variant 0.11
rpsA 1833876 p.Ala112Asp missense_variant 0.22
rpsA 1833914 p.Ala125Ser missense_variant 0.33
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918650 c.711C>T synonymous_variant 0.14
ndh 2102827 c.216C>A synonymous_variant 0.14
katG 2154168 p.Glu648Asp missense_variant 0.22
katG 2155506 c.606C>A synonymous_variant 0.18
katG 2156042 p.Gly24Cys missense_variant 0.22
PPE35 2167909 p.Gly902* stop_gained 0.14
PPE35 2169320 p.Leu431Phe missense_variant 0.19
PPE35 2170290 p.Ala108Glu missense_variant 0.17
Rv1979c 2223051 p.Glu38Asp missense_variant 0.89
Rv1979c 2223078 c.87C>T synonymous_variant 0.22
Rv1979c 2223156 c.9C>A synonymous_variant 0.15
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518623 p.Ala170Asp missense_variant 0.2
kasA 2518919 p.Gly269Ser missense_variant 1.0
eis 2714477 p.Arg286Ser missense_variant 0.15
eis 2714712 c.621G>T synonymous_variant 0.12
eis 2714937 c.396G>T synonymous_variant 0.12
eis 2715000 c.333C>A synonymous_variant 0.17
eis 2715206 p.Asp43Asn missense_variant 0.15
eis 2715441 c.-109C>T upstream_gene_variant 0.12
folC 2746903 c.696G>T synonymous_variant 0.18
folC 2747001 p.Asp200Tyr missense_variant 0.17
pepQ 2859603 c.816G>T synonymous_variant 0.14
pepQ 2860247 p.Gly58Cys missense_variant 0.2
Rv2752c 3064809 c.1383C>T synonymous_variant 0.25
Rv2752c 3065385 p.Asn269Lys missense_variant 0.12
Rv2752c 3065657 p.Asp179His missense_variant 0.15
Rv2752c 3065824 p.Pro123Leu missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087201 p.Pro128Ser missense_variant 0.2
ald 3087271 p.Arg151Gln missense_variant 0.2
ald 3087441 p.Asp208Tyr missense_variant 0.14
ald 3087471 p.Arg218Cys missense_variant 0.18
ald 3087749 c.930C>A synonymous_variant 0.17
ald 3087813 p.Ala332Ser missense_variant 0.15
fbiD 3339556 p.Gly147Cys missense_variant 0.13
Rv3083 3448616 p.Arg38Pro missense_variant 0.1
Rv3083 3449339 p.Arg279His missense_variant 0.15
Rv3083 3449856 p.Met451Ile missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474228 c.222C>A synonymous_variant 0.12
fprA 3475285 p.Asp427Asn missense_variant 0.18
Rv3236c 3612178 c.939C>A synonymous_variant 0.12
Rv3236c 3612454 c.663G>A synonymous_variant 0.12
Rv3236c 3613249 c.-135_-134delCG upstream_gene_variant 0.17
fbiB 3642711 p.Leu393Val missense_variant 0.14
rpoA 3877531 p.Ala326Asp missense_variant 0.14
rpoA 3878386 p.Thr41Asn missense_variant 0.2
ddn 3986725 c.-119G>T upstream_gene_variant 0.18
ddn 3986745 c.-99A>G upstream_gene_variant 0.14
ddn 3987074 c.231C>A synonymous_variant 0.12
clpC1 4038203 p.Lys834Asn missense_variant 0.14
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038389 c.2316G>A synonymous_variant 0.22
clpC1 4038428 c.2277G>T synonymous_variant 0.18
clpC1 4039013 c.1692G>A synonymous_variant 0.17
clpC1 4039141 c.1563delA frameshift_variant 0.17
clpC1 4039474 p.Arg411Trp missense_variant 0.17
clpC1 4039886 c.819C>A synonymous_variant 0.13
clpC1 4040856 c.-152G>T upstream_gene_variant 0.14
panD 4044009 c.273G>T synonymous_variant 0.12
embC 4239846 c.-17C>T upstream_gene_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243383 p.Ala51Ser missense_variant 0.17
embA 4243782 p.Gly184Trp missense_variant 0.18
embA 4243791 p.Ala187Ser missense_variant 0.18
embA 4243908 p.Arg226Trp missense_variant 0.18
embA 4244770 p.Gly513Val missense_variant 0.2
embA 4244878 p.Ala549Asp missense_variant 0.29
embA 4245195 p.Ile655Phe missense_variant 0.13
embB 4246256 c.-258G>T upstream_gene_variant 0.22
embB 4246566 p.Gly18Val missense_variant 0.25
embB 4246976 p.Ala155Ser missense_variant 0.12
embB 4247203 c.690C>A synonymous_variant 0.33
embB 4248128 p.Arg539Trp missense_variant 0.14
embB 4248155 p.Leu548Ile missense_variant 0.14
embB 4248855 p.Gly781Asp missense_variant 0.18
embB 4249374 p.Ser954Trp missense_variant 0.11
aftB 4268662 p.Thr59Ala missense_variant 0.15
aftB 4268811 p.Ser9Leu missense_variant 0.22
ubiA 4269271 p.Val188Ala missense_variant 1.0
ubiA 4269684 p.Glu50Asp missense_variant 0.22
ubiA 4269983 c.-150C>T upstream_gene_variant 0.22
ethA 4326762 p.Val238Leu missense_variant 0.13
ethA 4327328 p.Arg49His missense_variant 0.18
ethA 4327425 p.Val17Ile missense_variant 0.12
ethR 4327964 p.Ser139* stop_gained 0.2
ethR 4328185 p.Gly213Cys missense_variant 0.15
ethA 4328312 c.-839C>T upstream_gene_variant 0.15
ethA 4328398 c.-925C>T upstream_gene_variant 0.22
whiB6 4338215 p.Gly103Cys missense_variant 0.33
whiB6 4338321 c.201C>A synonymous_variant 0.17
whiB6 4338361 p.Arg54Leu missense_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407563 p.Gly214Trp missense_variant 0.22
gid 4408156 p.Leu16Arg missense_variant 1.0
gid 4408185 c.18C>A synonymous_variant 0.18
gid 4407912 c.160_290del frameshift_variant 1.0