TB-Profiler result

Run: ERR2843536
Summary

Run ID: ERR2843536

Sample name:

Date: 31-03-2023 23:53:52

Number of reads: 4767359

Percentage reads mapped: 85.02

Strain: lineage2.2.1

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
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
rpsL 781822 p.Lys88Arg missense_variant 0.11 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 5626 c.387C>T synonymous_variant 0.2
gyrB 6423 p.Trp395* stop_gained 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7571 c.270G>T synonymous_variant 0.13
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7640 p.Gln113His missense_variant 0.2
gyrA 7807 p.Arg169Gln missense_variant 0.15
gyrA 7835 c.534A>T synonymous_variant 0.18
gyrA 8554 p.Arg418Leu missense_variant 0.18
gyrA 8588 c.1288delA frameshift_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9567 p.Asp756Tyr missense_variant 0.17
fgd1 491409 c.627G>A synonymous_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575704 c.357T>G synonymous_variant 0.22
mshA 575785 c.438T>G synonymous_variant 0.17
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 575951 p.Gly202Trp missense_variant 0.2
mshA 576108 p.Ala254Gly missense_variant 0.21
ccsA 620534 p.Met215Thr missense_variant 0.12
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 759852 p.Ser16Cys missense_variant 0.13
rpoB 759998 p.Trp64Cys missense_variant 0.15
rpoB 760790 c.984C>T synonymous_variant 0.13
rpoB 761572 p.Pro589Arg missense_variant 0.18
rpoB 761594 c.1788C>T synonymous_variant 0.18
rpoB 761856 p.Val684Met missense_variant 0.15
rpoB 761865 p.Gly687Ser missense_variant 0.15
rpoB 762993 p.Gly1063Trp missense_variant 0.21
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765833 p.Gly822Cys missense_variant 0.14
rpoC 766859 c.3490C>A synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775652 c.2829C>T synonymous_variant 0.12
mmpL5 775726 c.2755C>T synonymous_variant 0.12
mmpL5 775736 c.2745C>G synonymous_variant 0.15
mmpL5 775741 c.2740C>T synonymous_variant 0.15
mmpL5 775742 c.2739C>T synonymous_variant 0.15
mmpL5 775747 p.Met912Leu missense_variant 0.14
mmpL5 775834 p.Ala883Thr missense_variant 0.2
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpL5 777815 c.666C>A synonymous_variant 0.13
mmpL5 777991 p.Glu164Lys missense_variant 0.15
mmpL5 778537 c.-57G>A upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304428 c.1498C>A synonymous_variant 0.25
fbiC 1304524 p.Ala532Ser missense_variant 0.25
Rv1258c 1406245 p.Leu366Met missense_variant 0.2
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416281 p.Arg356Gln missense_variant 0.12
embR 1416459 p.Ser297Thr missense_variant 0.15
embR 1416505 c.843C>T synonymous_variant 0.14
embR 1416906 p.Pro148Ser missense_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471945 n.100G>A non_coding_transcript_exon_variant 0.12
rrs 1472094 n.249T>A non_coding_transcript_exon_variant 0.2
rrs 1472100 n.255T>C non_coding_transcript_exon_variant 0.3
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.3
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.27
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.31
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.31
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.29
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.36
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.36
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.46
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.5
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.43
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.43
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.46
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.38
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.33
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.27
rrs 1472378 n.533G>A non_coding_transcript_exon_variant 0.14
rrs 1472423 n.578G>A non_coding_transcript_exon_variant 0.18
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.22
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.22
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.27
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.25
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.25
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.25
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.25
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.33
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.41
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.41
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.39
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.52
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.58
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.7
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.67
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.67
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.64
rrs 1472669 n.824_825insTAG non_coding_transcript_exon_variant 0.62
rrs 1472677 n.832C>G non_coding_transcript_exon_variant 0.62
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.57
rrs 1472679 n.834_835insAC non_coding_transcript_exon_variant 0.62
rrs 1472684 n.841_846delGATCCG non_coding_transcript_exon_variant 0.62
rrs 1472697 n.852T>A non_coding_transcript_exon_variant 0.62
rrs 1472700 n.855C>T non_coding_transcript_exon_variant 0.62
rrs 1472705 n.860G>A non_coding_transcript_exon_variant 0.62
rrs 1472708 n.863T>G non_coding_transcript_exon_variant 0.67
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.73
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.73
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.83
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.83
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.83
rrs 1472767 n.922G>A non_coding_transcript_exon_variant 0.6
rrs 1472779 n.934G>A non_coding_transcript_exon_variant 0.43
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.43
rrs 1472786 n.941C>T non_coding_transcript_exon_variant 0.38
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.3
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.33
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.3
rrs 1472954 n.1109T>A non_coding_transcript_exon_variant 0.54
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.54
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.54
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.54
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.54
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.38
rrs 1472974 n.1129A>G non_coding_transcript_exon_variant 0.18
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.46
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.56
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.54
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.52
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.52
rrs 1472992 n.1147A>T non_coding_transcript_exon_variant 0.52
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.53
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.53
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.53
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.53
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.5
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.28
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.24
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.19
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.15
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.15
rrs 1473120 n.1275C>A non_coding_transcript_exon_variant 0.17
rrs 1473177 n.1332G>A non_coding_transcript_exon_variant 0.18
rrs 1473179 n.1334C>T non_coding_transcript_exon_variant 0.18
rrs 1473192 n.1347A>G non_coding_transcript_exon_variant 0.18
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.15
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.19
rrs 1473352 n.1507C>T non_coding_transcript_exon_variant 0.17
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.4
rrl 1473899 n.242A>C non_coding_transcript_exon_variant 0.4
rrl 1473905 n.248T>C non_coding_transcript_exon_variant 0.4
rrl 1473926 n.269G>C non_coding_transcript_exon_variant 0.5
rrl 1474758 n.1101G>A non_coding_transcript_exon_variant 0.22
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.38
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.38
rrl 1474780 n.1123C>T non_coding_transcript_exon_variant 0.33
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.33
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.54
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.62
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.67
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.69
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.72
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.63
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.68
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.6
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.47
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.39
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.35
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.25
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.2
rrl 1474927 n.1271delC non_coding_transcript_exon_variant 0.2
rrl 1474931 n.1274G>A non_coding_transcript_exon_variant 0.2
rrl 1475167 n.1510T>A non_coding_transcript_exon_variant 0.33
rrl 1475672 n.2015C>G non_coding_transcript_exon_variant 0.2
rrl 1475673 n.2016T>C non_coding_transcript_exon_variant 0.2
rrl 1475687 n.2030C>T non_coding_transcript_exon_variant 0.27
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.3
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.3
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.33
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.22
rrl 1475927 n.2270G>A non_coding_transcript_exon_variant 0.25
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.2
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.43
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.5
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.44
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.67
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.63
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.63
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.71
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.71
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.71
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.67
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.63
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.67
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.71
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.62
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.67
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.68
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.79
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.83
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 1476372 n.2715T>C non_coding_transcript_exon_variant 0.81
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.82
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.79
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.79
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.8
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.79
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.76
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.72
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.56
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.45
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.41
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.41
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.44
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.41
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.41
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.41
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.41
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.43
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.43
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.43
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.43
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.46
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.4
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.4
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.43
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.41
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.21
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.12
fabG1 1673557 p.His40Asn missense_variant 0.17
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102039 p.Gly335Val missense_variant 0.15
katG 2154245 p.Glu623Lys missense_variant 0.15
katG 2154254 p.Ser620Gly missense_variant 0.15
katG 2154521 p.Ala531Ser missense_variant 0.14
katG 2154594 c.1518G>A synonymous_variant 0.4
katG 2154653 p.Asp487His missense_variant 0.25
katG 2154673 p.Ala480Glu missense_variant 0.13
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155355 p.Arg253Trp missense_variant 0.17
katG 2156369 c.-258C>A upstream_gene_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2169205 p.Ile470Val missense_variant 0.14
PPE35 2169348 p.Phe422Ser missense_variant 0.14
PPE35 2169375 p.Asn413Thr missense_variant 0.11
Rv1979c 2223211 c.-47G>A upstream_gene_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289243 c.-2G>A upstream_gene_variant 0.14
kasA 2518364 p.Gln84* stop_gained 0.15
eis 2715313 p.Ser7Ile missense_variant 0.15
eis 2715355 c.-23G>A upstream_gene_variant 0.15
eis 2715414 c.-82C>A upstream_gene_variant 0.17
eis 2715534 c.-202C>T upstream_gene_variant 0.2
ahpC 2726084 c.-109C>T upstream_gene_variant 0.15
folC 2747027 p.Val191Gly missense_variant 0.25
folC 2747134 c.465C>T synonymous_variant 0.12
pepQ 2859902 p.Ser173Cys missense_variant 0.2
ribD 2986886 c.48G>A synonymous_variant 0.13
Rv2752c 3064686 p.Lys502Asn missense_variant 0.17
Rv2752c 3065488 p.Val235Asp missense_variant 0.18
thyA 3073771 p.Asp234Gly missense_variant 0.11
thyA 3074442 c.30C>T synonymous_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086865 p.Val16Met missense_variant 0.13
ald 3087284 c.465C>A synonymous_variant 0.17
fbiD 3339734 p.Ala206Gly missense_variant 0.3
Rv3083 3448889 p.Arg129Leu missense_variant 0.21
Rv3083 3449069 p.Ala189Glu missense_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474303 c.297C>A synonymous_variant 0.15
fprA 3475140 c.1134C>A synonymous_variant 0.14
whiB7 3568427 p.Arg85Ser missense_variant 0.13
whiB7 3568428 c.252A>G synonymous_variant 0.27
whiB7 3568516 p.Ala55Val missense_variant 0.17
Rv3236c 3612068 p.Gly350Val missense_variant 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3641108 p.Gly189Val missense_variant 0.13
fbiA 3641113 p.Glu191* stop_gained 0.14
fbiB 3641334 c.-201G>C upstream_gene_variant 0.18
fbiB 3641657 c.123C>A synonymous_variant 0.13
fbiB 3641665 p.Asp44Gly missense_variant 0.13
fbiB 3641815 p.Ile94Thr missense_variant 0.12
fbiB 3642722 c.1188C>T synonymous_variant 0.18
rpoA 3878052 c.456C>T synonymous_variant 0.17
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 1.0
ddn 3986713 c.-131C>G upstream_gene_variant 0.15
clpC1 4038990 p.Gly572Asp missense_variant 0.12
clpC1 4039004 c.1701C>A synonymous_variant 0.18
clpC1 4039302 p.Trp468Leu missense_variant 0.13
clpC1 4039988 c.717C>A synonymous_variant 0.13
clpC1 4040852 c.-148C>T upstream_gene_variant 0.29
embC 4240192 c.330C>A synonymous_variant 0.18
embC 4241300 p.Ala480Pro missense_variant 0.15
embC 4241311 c.1449C>A synonymous_variant 0.18
embC 4241366 c.1505delT frameshift_variant 0.22
embC 4241468 p.Ala536Thr missense_variant 0.18
embC 4241745 p.Phe628Ser missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245063 c.1831C>T synonymous_variant 0.13
embA 4245511 p.Pro760Leu missense_variant 0.14
embB 4247683 c.1170C>T synonymous_variant 0.13
embB 4247743 c.1230C>T synonymous_variant 0.13
embB 4248569 p.Leu686Met missense_variant 0.14
embB 4248613 c.2100C>T synonymous_variant 0.13
embB 4249105 c.2592C>A synonymous_variant 0.2
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267985 c.852C>T synonymous_variant 0.15
ethA 4326145 c.1329G>A synonymous_variant 0.13
ethA 4326270 p.Val402Phe missense_variant 0.13
ethA 4326774 p.Ala234Ser missense_variant 0.18
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407643 p.Arg187Lys missense_variant 0.17
gid 4407927 p.Glu92Asp missense_variant 1.0