TB-Profiler result

Run: ERR4822101
Summary

Run ID: ERR4822101

Sample name:

Date: 01-04-2023 17:38:20

Number of reads: 2202581

Percentage reads mapped: 78.9

Strain: lineage4.1.3;lineage1.1.2

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
lineage4 Euro-American LAM;T;S;X;H None 0.54
lineage1 Indo-Oceanic EAI RD239 0.49
lineage4.1 Euro-American T;X;H None 0.5
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.47
lineage4.1.3 Euro-American T;X;H None 0.44
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.52
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 6112 p.Met291Ile missense_variant 0.25
gyrB 6124 c.885C>T synonymous_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7391 c.90C>T synonymous_variant 0.17
gyrA 7394 c.93T>C synonymous_variant 0.18
gyrA 7427 c.126G>C synonymous_variant 0.18
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8435 c.1134C>G synonymous_variant 0.54
gyrA 8452 p.Ala384Val missense_variant 0.57
gyrA 9143 c.1842T>C synonymous_variant 0.49
gyrA 9191 c.1890G>C synonymous_variant 0.13
gyrA 9200 c.1899A>G synonymous_variant 0.14
gyrA 9204 p.Ser635Thr missense_variant 0.14
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490812 c.30A>G synonymous_variant 0.14
fgd1 490815 c.33G>C synonymous_variant 0.14
fgd1 490827 c.45C>T synonymous_variant 0.14
fgd1 490851 c.69A>T synonymous_variant 0.13
fgd1 490868 p.Ala29Gly missense_variant 0.15
fgd1 491313 c.531C>G synonymous_variant 0.15
fgd1 491319 c.537G>C synonymous_variant 0.17
fgd1 491742 c.960T>C synonymous_variant 0.47
mshA 575376 p.Ser10Leu missense_variant 0.65
rpoB 760196 c.390C>G synonymous_variant 0.16
rpoB 760235 c.429T>C synonymous_variant 0.14
rpoB 760646 c.840C>G synonymous_variant 0.13
rpoB 760655 c.849A>G synonymous_variant 0.14
rpoB 760661 c.855A>C synonymous_variant 0.14
rpoB 760674 c.868T>C synonymous_variant 0.17
rpoB 760679 c.873A>G synonymous_variant 0.18
rpoB 760683 c.877T>C synonymous_variant 0.18
rpoB 761180 c.1374A>C synonymous_variant 0.14
rpoB 761189 c.1383T>C synonymous_variant 0.14
rpoB 761195 c.1389G>C synonymous_variant 0.15
rpoB 761219 c.1413G>C synonymous_variant 0.16
rpoB 761249 c.1443A>G synonymous_variant 0.2
rpoB 761255 c.1449T>G synonymous_variant 0.19
rpoB 761261 c.1455G>T synonymous_variant 0.17
rpoB 761306 c.1500C>G synonymous_variant 0.18
rpoB 761312 c.1506G>C synonymous_variant 0.19
rpoB 761327 c.1521A>G synonymous_variant 0.17
rpoB 761330 c.1524G>C synonymous_variant 0.17
rpoB 761354 c.1548C>T synonymous_variant 0.13
rpoB 761360 c.1554T>C synonymous_variant 0.13
rpoB 761570 c.1764T>C synonymous_variant 0.13
rpoB 761573 c.1767C>G synonymous_variant 0.15
rpoB 761615 c.1809A>C synonymous_variant 0.15
rpoB 761636 c.1830G>T synonymous_variant 0.14
rpoB 761948 c.2142G>C synonymous_variant 0.13
rpoB 762008 c.2202C>T synonymous_variant 0.16
rpoB 762053 c.2247T>C synonymous_variant 0.16
rpoB 762083 c.2277T>C synonymous_variant 0.13
rpoB 762284 c.2478G>C synonymous_variant 0.16
rpoB 762293 c.2487T>C synonymous_variant 0.16
rpoB 762338 c.2532T>C synonymous_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.46
rpoC 763040 c.-330C>G upstream_gene_variant 0.14
rpoC 763528 c.159G>A synonymous_variant 0.15
rpoC 763546 c.177A>G synonymous_variant 0.17
rpoC 763570 c.201G>C synonymous_variant 0.16
rpoC 763594 c.225C>T synonymous_variant 0.16
rpoC 763702 c.333C>G synonymous_variant 0.15
rpoC 763717 c.348T>C synonymous_variant 0.15
rpoC 763884 p.Ala172Val missense_variant 0.57
rpoC 763886 c.517C>A synonymous_variant 0.6
rpoC 764083 c.714A>G synonymous_variant 0.15
rpoC 764098 c.729A>G synonymous_variant 0.15
rpoC 764131 c.762T>C synonymous_variant 0.14
rpoC 764140 c.771C>T synonymous_variant 0.14
rpoC 764215 c.846A>G synonymous_variant 0.13
rpoC 764236 c.867G>A synonymous_variant 0.19
rpoC 764248 c.879C>G synonymous_variant 0.17
rpoC 764257 c.888G>C synonymous_variant 0.17
rpoC 764266 c.897T>C synonymous_variant 0.14
rpoC 764269 c.900G>C synonymous_variant 0.14
rpoC 764278 c.909A>G synonymous_variant 0.15
rpoC 764431 c.1062G>C synonymous_variant 0.14
rpoC 764434 c.1065A>G synonymous_variant 0.14
rpoC 764497 c.1128A>G synonymous_variant 0.15
rpoC 764510 c.1141C>T synonymous_variant 0.12
rpoC 764536 c.1167G>C synonymous_variant 0.14
rpoC 764539 c.1170C>G synonymous_variant 0.14
rpoC 764554 c.1185C>T synonymous_variant 0.22
rpoC 764560 c.1191T>C synonymous_variant 0.19
rpoC 764566 c.1197C>G synonymous_variant 0.25
rpoC 764575 c.1206T>G synonymous_variant 0.22
rpoC 764581 c.1212T>C synonymous_variant 0.17
rpoC 764593 c.1224C>T synonymous_variant 0.22
rpoC 764602 c.1233C>T synonymous_variant 0.13
rpoC 764611 c.1242G>T synonymous_variant 0.21
rpoC 764752 c.1383G>C synonymous_variant 0.17
rpoC 764764 c.1395T>C synonymous_variant 0.18
rpoC 764809 c.1440C>T synonymous_variant 0.13
rpoC 764815 c.1446A>G synonymous_variant 0.17
rpoC 764858 c.1489T>C synonymous_variant 0.14
rpoC 764872 c.1503A>G synonymous_variant 0.13
rpoC 764911 c.1542A>G synonymous_variant 0.16
rpoC 764932 c.1563C>A synonymous_variant 0.18
rpoC 764935 c.1566T>C synonymous_variant 0.13
rpoC 764948 c.1579T>C synonymous_variant 0.16
rpoC 764968 c.1599T>C synonymous_variant 0.16
rpoC 765150 p.Gly594Glu missense_variant 0.53
rpoC 765171 p.Pro601Leu missense_variant 0.42
rpoC 765421 c.2052C>G synonymous_variant 0.16
rpoC 765478 c.2109T>C synonymous_variant 0.2
rpoC 765499 c.2130C>G synonymous_variant 0.25
rpoC 765529 c.2160C>T synonymous_variant 0.25
rpoC 765541 c.2172C>G synonymous_variant 0.28
rpoC 765553 c.2184C>T synonymous_variant 0.27
rpoC 765556 c.2187G>C synonymous_variant 0.24
rpoC 765559 c.2190G>C synonymous_variant 0.25
rpoC 765580 c.2211G>C synonymous_variant 0.23
rpoC 765613 p.His748Gln missense_variant 0.2
rpoC 765625 c.2256C>G synonymous_variant 0.17
rpoC 765631 p.Asp754Glu missense_variant 0.16
rpoC 765700 c.2331T>C synonymous_variant 0.16
rpoC 765886 c.2517C>G synonymous_variant 0.14
rpoC 765937 c.2568T>C synonymous_variant 0.14
rpoC 765967 c.2598C>T synonymous_variant 0.16
rpoC 765982 c.2613C>G synonymous_variant 0.17
rpoC 765994 c.2625A>T synonymous_variant 0.18
rpoC 766021 c.2652G>C synonymous_variant 0.15
rpoC 766027 c.2658G>C synonymous_variant 0.16
rpoC 766030 c.2661C>G synonymous_variant 0.14
rpoC 767059 c.3690T>G synonymous_variant 0.13
rpoC 767098 c.3729T>C synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.36
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.5
fbiC 1303914 c.984C>G synonymous_variant 0.17
fbiC 1303920 c.990C>T synonymous_variant 0.18
fbiC 1304142 c.1212G>C synonymous_variant 0.15
fbiC 1304161 p.Arg411Ser missense_variant 0.15
fbiC 1304169 c.1239T>C synonymous_variant 0.14
fbiC 1304174 p.Val415Ala missense_variant 0.14
fbiC 1304184 c.1254G>C synonymous_variant 0.15
fbiC 1304187 c.1257T>C synonymous_variant 0.15
fbiC 1304208 c.1278C>T synonymous_variant 0.12
fbiC 1304610 c.1680C>T synonymous_variant 0.44
fbiC 1304784 c.1854T>C synonymous_variant 0.15
fbiC 1304808 c.1878C>G synonymous_variant 0.14
fbiC 1304811 c.1881C>G synonymous_variant 0.15
fbiC 1304817 c.1887T>C synonymous_variant 0.18
fbiC 1304829 c.1899T>C synonymous_variant 0.25
fbiC 1304832 c.1902C>T synonymous_variant 0.19
fbiC 1304853 c.1923C>G synonymous_variant 0.12
fbiC 1304856 c.1926C>G synonymous_variant 0.33
fbiC 1304869 c.1939C>T synonymous_variant 0.15
fbiC 1304875 p.Ile649Val missense_variant 0.16
fbiC 1304883 p.Glu651Asp missense_variant 0.15
fbiC 1304891 p.Ile654Thr missense_variant 0.15
fbiC 1304893 p.Gly655Ser missense_variant 0.15
fbiC 1304907 c.1977C>G synonymous_variant 0.15
fbiC 1304910 c.1980G>C synonymous_variant 0.15
fbiC 1304916 c.1986T>C synonymous_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 0.33
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.13
rrs 1472251 n.406G>T non_coding_transcript_exon_variant 0.13
rrs 1472252 n.407G>A non_coding_transcript_exon_variant 0.13
rrs 1472256 n.411T>A non_coding_transcript_exon_variant 0.14
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.14
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.28
rrs 1472754 n.909G>T non_coding_transcript_exon_variant 0.19
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.23
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.23
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.16
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25
rrl 1473660 n.3G>A non_coding_transcript_exon_variant 0.37
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.23
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.14
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.14
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.16
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.16
rrl 1475170 n.1513A>T non_coding_transcript_exon_variant 0.2
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.13
rpsA 1833595 c.54T>C synonymous_variant 0.13
rpsA 1833661 c.120A>G synonymous_variant 0.15
rpsA 1833787 c.246C>G synonymous_variant 0.16
rpsA 1833802 c.261A>G synonymous_variant 0.15
rpsA 1833841 c.300C>G synonymous_variant 0.13
rpsA 1833847 c.306C>G synonymous_variant 0.15
rpsA 1833856 c.315A>G synonymous_variant 0.14
rpsA 1834528 c.987T>C synonymous_variant 0.14
rpsA 1834609 c.1068T>C synonymous_variant 0.13
rpsA 1834633 c.1092A>G synonymous_variant 0.15
rpsA 1834639 c.1098T>C synonymous_variant 0.15
rpsA 1834690 c.1149T>C synonymous_variant 0.15
rpsA 1834732 c.1191T>C synonymous_variant 0.15
rpsA 1834738 c.1197A>G synonymous_variant 0.13
rpsA 1834753 c.1212T>C synonymous_variant 0.15
rpsA 1834765 p.Glu408Asp missense_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 0.41
PPE35 2167983 p.Gly877Asp missense_variant 0.31
Rv1979c 2222308 p.Asp286Gly missense_variant 0.51
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.5
ahpC 2726051 c.-142G>A upstream_gene_variant 0.5
Rv2752c 3064632 c.1560C>T synonymous_variant 0.42
thyX 3067355 c.591A>C synonymous_variant 0.13
thyX 3067367 c.579G>C synonymous_variant 0.15
thyX 3067373 c.573C>G synonymous_variant 0.15
thyX 3067376 c.570G>A synonymous_variant 0.13
thyX 3067391 c.555G>C synonymous_variant 0.14
thyX 3067394 c.552G>C synonymous_variant 0.15
thyX 3067439 c.507A>G synonymous_variant 0.17
thyX 3067445 c.501C>G synonymous_variant 0.16
thyX 3067457 c.489C>G synonymous_variant 0.18
thyX 3067465 p.Ile161Val missense_variant 0.18
thyX 3067475 c.471A>G synonymous_variant 0.19
thyX 3067490 c.456C>G synonymous_variant 0.2
thyX 3067493 c.453A>G synonymous_variant 0.2
thyX 3067515 p.Ser144Thr missense_variant 0.13
thyX 3067685 c.261A>C synonymous_variant 0.14
thyA 3073860 c.612C>G synonymous_variant 0.14
thyA 3073872 p.Ile200Met missense_variant 0.13
thyA 3073920 c.552C>G synonymous_variant 0.15
thyA 3073929 c.543T>C synonymous_variant 0.12
thyA 3073989 c.483T>C synonymous_variant 0.12
thyA 3074004 c.468T>C synonymous_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 0.98
Rv3083 3448714 p.Asp71His missense_variant 0.42
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.97
fprA 3474597 c.591C>A synonymous_variant 0.56
fprA 3475159 p.Asn385Asp missense_variant 0.49
rpoA 3877613 p.Ile299Val missense_variant 0.12
rpoA 3877656 c.852T>G synonymous_variant 0.14
rpoA 3877668 c.840A>G synonymous_variant 0.15
rpoA 3877679 p.Ala277Ser missense_variant 0.17
rpoA 3877686 c.822A>G synonymous_variant 0.16
rpoA 3877692 c.816G>C synonymous_variant 0.19
rpoA 3877704 c.804G>C synonymous_variant 0.19
rpoA 3877743 c.765T>C synonymous_variant 0.2
rpoA 3877764 c.744C>G synonymous_variant 0.18
rpoA 3877770 c.738A>G synonymous_variant 0.19
rpoA 3877776 c.732T>C synonymous_variant 0.15
rpoA 3877782 c.726T>C synonymous_variant 0.13
rpoA 3877848 c.660C>T synonymous_variant 0.13
rpoA 3877866 c.642G>C synonymous_variant 0.14
rpoA 3877875 c.633T>G synonymous_variant 0.16
rpoA 3877878 c.630G>C synonymous_variant 0.15
rpoA 3877890 c.618C>T synonymous_variant 0.13
rpoA 3877896 c.612G>C synonymous_variant 0.13
rpoA 3877905 c.603A>G synonymous_variant 0.18
rpoA 3877920 c.588G>C synonymous_variant 0.19
rpoA 3877923 c.585C>T synonymous_variant 0.19
rpoA 3878217 c.291A>G synonymous_variant 0.15
clpC1 4038770 c.1935C>T synonymous_variant 0.15
clpC1 4038773 c.1932T>C synonymous_variant 0.15
clpC1 4038782 c.1923G>C synonymous_variant 0.16
clpC1 4038812 c.1893T>C synonymous_variant 0.21
clpC1 4038845 c.1860G>C synonymous_variant 0.18
clpC1 4039178 c.1527G>C synonymous_variant 0.18
clpC1 4039183 c.1522T>C synonymous_variant 0.17
clpC1 4039274 c.1431G>C synonymous_variant 0.15
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4039562 c.1143C>G synonymous_variant 0.13
clpC1 4039589 c.1116G>C synonymous_variant 0.13
clpC1 4039616 c.1089G>C synonymous_variant 0.14
clpC1 4039622 c.1083C>T synonymous_variant 0.13
clpC1 4039661 c.1044T>G synonymous_variant 0.12
clpC1 4039694 c.1011G>C synonymous_variant 0.16
clpC1 4039724 c.981A>G synonymous_variant 0.15
clpC1 4039952 c.753T>C synonymous_variant 0.15
clpC1 4039979 c.726C>G synonymous_variant 0.22
clpC1 4040033 c.672G>C synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 0.43
embC 4240671 p.Thr270Ile missense_variant 0.46
embC 4241042 p.Asn394Asp missense_variant 0.51
embC 4241719 c.1857G>C synonymous_variant 0.12
embC 4241727 p.Phe622Tyr missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.5
embA 4243848 p.Val206Met missense_variant 0.68
embA 4245083 c.1851A>C synonymous_variant 0.15
embA 4245089 c.1857G>C synonymous_variant 0.19
embA 4245092 c.1860C>G synonymous_variant 0.18
embA 4245101 c.1869G>C synonymous_variant 0.2
embA 4245137 c.1905T>C synonymous_variant 0.23
embA 4245146 c.1914G>A synonymous_variant 0.23
embA 4245149 c.1917C>G synonymous_variant 0.24
embA 4245153 p.Ile641Val missense_variant 0.21
embA 4245182 c.1950T>C synonymous_variant 0.13
embA 4245969 p.Pro913Ser missense_variant 0.61
embB 4247356 c.843C>T synonymous_variant 0.53
embB 4247646 p.Glu378Ala missense_variant 0.56
aftB 4268602 p.Leu79Met missense_variant 0.12
aftB 4268608 p.Met77Leu missense_variant 0.12
aftB 4268612 c.225G>C synonymous_variant 0.12
aftB 4268618 c.219G>C synonymous_variant 0.13
aftB 4268626 p.Gly71Ser missense_variant 0.13
aftB 4268683 p.Gly52Ser missense_variant 0.33
ubiA 4269387 p.Glu149Asp missense_variant 0.48
aftB 4269606 c.-770T>C upstream_gene_variant 0.51
whiB6 4338441 p.Tyr27* stop_gained 0.36
whiB6 4338449 p.Ala25Pro missense_variant 0.39
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.33
gid 4407588 c.615A>G synonymous_variant 0.36
gid 4407873 c.330G>T synonymous_variant 0.36