TB-Profiler result

Run: ERR4814683
Summary

Run ID: ERR4814683

Sample name:

Date: 01-04-2023 13:26:08

Number of reads: 2101136

Percentage reads mapped: 79.33

Strain: lineage4.1.3;lineage4.1.2.1;lineage1.1.2

Drug-resistance: Sensitive

Download CSV Download TXT Download PDF Download JSON
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 0.75
lineage1 Indo-Oceanic EAI RD239 0.25
lineage4.1 Euro-American T;X;H None 0.74
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.2
lineage4.1.3 Euro-American T;X;H None 0.54
lineage1.1.2 Indo-Oceanic EAI3;EAI5 RD239 0.27
lineage4.1.2 Euro-American T;H None 0.26
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.21
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 0.18
gyrB 6124 c.885C>T synonymous_variant 0.2
gyrB 6798 p.Gly520Ala missense_variant 0.15
gyrA 6841 c.-461T>C upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7475 c.174A>G synonymous_variant 0.13
gyrA 7480 p.Phe60Tyr missense_variant 0.18
gyrA 7484 c.183T>C synonymous_variant 0.19
gyrA 7523 c.222C>G synonymous_variant 0.14
gyrA 7526 c.225G>C synonymous_variant 0.14
gyrA 7532 c.231T>G synonymous_variant 0.13
gyrA 7571 c.270G>C synonymous_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7793 c.492G>C synonymous_variant 0.16
gyrA 7799 c.498A>G synonymous_variant 0.15
gyrA 7814 c.513C>G synonymous_variant 0.13
gyrA 8435 c.1134C>G synonymous_variant 0.15
gyrA 8452 p.Ala384Val missense_variant 0.16
gyrA 8852 c.1551T>C synonymous_variant 0.14
gyrA 8870 c.1569G>C synonymous_variant 0.16
gyrA 8897 c.1596T>C synonymous_variant 0.15
gyrA 9143 c.1842T>C synonymous_variant 0.32
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 0.2
fgd1 491742 c.960T>C synonymous_variant 0.23
mshA 575376 p.Ser10Leu missense_variant 0.24
mshA 575679 p.Asn111Ser missense_variant 0.25
rpoB 760115 c.309C>T synonymous_variant 0.26
rpoB 760184 c.378A>G synonymous_variant 0.19
rpoB 760196 c.390C>G synonymous_variant 0.17
rpoB 760223 c.417T>C synonymous_variant 0.2
rpoB 760235 c.429T>C synonymous_variant 0.19
rpoB 760406 c.600G>C synonymous_variant 0.16
rpoB 760430 c.624T>C synonymous_variant 0.16
rpoB 760475 c.669A>G synonymous_variant 0.16
rpoB 760591 p.Val262Ala missense_variant 0.18
rpoB 760611 c.805T>C synonymous_variant 0.16
rpoB 760634 c.828T>C synonymous_variant 0.15
rpoB 760646 c.840C>G synonymous_variant 0.21
rpoB 760655 c.849A>G synonymous_variant 0.18
rpoB 760661 c.855A>C synonymous_variant 0.19
rpoB 760674 c.868T>C synonymous_variant 0.15
rpoB 760679 c.873A>G synonymous_variant 0.15
rpoB 760683 c.877T>C synonymous_variant 0.17
rpoB 760946 c.1140A>G synonymous_variant 0.15
rpoB 760982 c.1176G>C synonymous_variant 0.18
rpoB 760985 c.1179G>C synonymous_variant 0.17
rpoB 760991 c.1185G>C synonymous_variant 0.15
rpoB 761006 c.1200C>G synonymous_variant 0.16
rpoB 761015 c.1209G>C synonymous_variant 0.17
rpoB 761021 c.1215G>C synonymous_variant 0.15
rpoB 761027 c.1221A>G synonymous_variant 0.15
rpoB 761165 c.1359G>C synonymous_variant 0.17
rpoB 761180 c.1374A>C synonymous_variant 0.24
rpoB 761189 c.1383T>C synonymous_variant 0.22
rpoB 761195 c.1389G>C synonymous_variant 0.23
rpoB 761219 c.1413G>C synonymous_variant 0.21
rpoB 761249 c.1443A>G synonymous_variant 0.19
rpoB 761255 c.1449T>G synonymous_variant 0.16
rpoB 761570 c.1764T>C synonymous_variant 0.13
rpoB 761573 c.1767C>G synonymous_variant 0.14
rpoB 761579 c.1773G>C synonymous_variant 0.18
rpoB 761612 c.1806G>T synonymous_variant 0.14
rpoB 761615 c.1809A>C synonymous_variant 0.23
rpoB 761636 c.1830G>T synonymous_variant 0.14
rpoB 762176 c.2370T>C synonymous_variant 0.13
rpoB 762233 c.2427G>C synonymous_variant 0.15
rpoB 762293 c.2487T>C synonymous_variant 0.14
rpoC 762929 c.-441G>C upstream_gene_variant 0.14
rpoC 762989 c.-381G>A upstream_gene_variant 0.13
rpoC 762995 c.-375G>T upstream_gene_variant 0.22
rpoC 763031 c.-339T>C upstream_gene_variant 0.28
rpoC 763040 c.-330C>G upstream_gene_variant 0.24
rpoC 763070 c.-300T>C upstream_gene_variant 0.22
rpoC 763085 c.-285C>G upstream_gene_variant 0.19
rpoC 763115 c.-255T>C upstream_gene_variant 0.21
rpoC 763136 c.-234C>T upstream_gene_variant 0.23
rpoC 763166 c.-204A>G upstream_gene_variant 0.18
rpoC 763528 c.159G>A synonymous_variant 0.14
rpoC 763546 c.177A>G synonymous_variant 0.21
rpoC 763570 c.201G>C synonymous_variant 0.24
rpoC 763594 c.225C>T synonymous_variant 0.31
rpoC 763618 c.249C>T synonymous_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 0.26
rpoC 763886 c.517C>A synonymous_variant 0.27
rpoC 764497 c.1128A>G synonymous_variant 0.15
rpoC 764506 c.1137C>T synonymous_variant 0.12
rpoC 764527 c.1158C>T synonymous_variant 0.19
rpoC 764539 c.1170C>G synonymous_variant 0.2
rpoC 764554 c.1185C>T synonymous_variant 0.21
rpoC 764566 c.1197C>G synonymous_variant 0.21
rpoC 764575 c.1206T>G synonymous_variant 0.21
rpoC 764593 c.1224C>T synonymous_variant 0.15
rpoC 764611 c.1242G>T synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.13
rpoC 764764 c.1395T>C synonymous_variant 0.13
rpoC 764815 c.1446A>G synonymous_variant 0.15
rpoC 764827 c.1458G>C synonymous_variant 0.16
rpoC 764858 c.1489T>C synonymous_variant 0.18
rpoC 764888 c.1519T>C synonymous_variant 0.14
rpoC 764911 c.1542A>G synonymous_variant 0.16
rpoC 764932 c.1563C>A synonymous_variant 0.17
rpoC 765150 p.Gly594Glu missense_variant 0.76
rpoC 765171 p.Pro601Leu missense_variant 0.3
rpoC 765421 c.2052C>G synonymous_variant 0.14
rpoC 765478 c.2109T>C synonymous_variant 0.2
rpoC 765499 c.2130C>G synonymous_variant 0.24
rpoC 765529 c.2160C>T synonymous_variant 0.25
rpoC 765541 c.2172C>G synonymous_variant 0.26
rpoC 765553 c.2184C>T synonymous_variant 0.18
rpoC 765556 c.2187G>C synonymous_variant 0.18
rpoC 765559 c.2190G>C synonymous_variant 0.17
rpoC 765580 c.2211G>C synonymous_variant 0.15
rpoC 765826 c.2457T>C synonymous_variant 0.15
rpoC 765835 c.2466C>T synonymous_variant 0.13
rpoC 765886 c.2517C>G synonymous_variant 0.19
rpoC 765937 c.2568T>C synonymous_variant 0.21
rpoC 765967 c.2598C>T synonymous_variant 0.12
rpoC 765982 c.2613C>G synonymous_variant 0.16
rpoC 765994 c.2625A>T synonymous_variant 0.16
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781421 c.-139C>A upstream_gene_variant 0.41
rpsL 781700 c.141G>C synonymous_variant 0.16
rpsL 781703 c.144G>T synonymous_variant 0.17
rpsL 781715 c.156T>C synonymous_variant 0.17
rpsL 781728 c.169T>C synonymous_variant 0.18
rpsL 781736 c.177T>C synonymous_variant 0.18
rpsL 781742 c.183C>T synonymous_variant 0.18
rpsL 781748 c.189C>G synonymous_variant 0.18
rpsL 781754 c.195G>C synonymous_variant 0.17
rpsL 781760 c.201T>C synonymous_variant 0.18
rpsL 781772 c.213C>A synonymous_variant 0.15
rpsL 781832 c.273T>C synonymous_variant 0.14
rpsL 781898 c.339A>T synonymous_variant 0.14
rpsL 781916 c.357T>C synonymous_variant 0.13
fbiC 1302741 c.-190G>A upstream_gene_variant 0.14
fbiC 1304127 c.1197A>G synonymous_variant 0.15
fbiC 1304132 p.Ala401Gly missense_variant 0.16
fbiC 1304142 c.1212G>C synonymous_variant 0.17
fbiC 1304161 p.Arg411Trp missense_variant 0.13
fbiC 1304174 p.Val415Ala missense_variant 0.15
fbiC 1304184 c.1254G>C synonymous_variant 0.16
fbiC 1304187 c.1257T>C synonymous_variant 0.16
fbiC 1304208 c.1278C>T synonymous_variant 0.17
fbiC 1304568 c.1638T>C synonymous_variant 0.14
fbiC 1304580 c.1650T>C synonymous_variant 0.16
fbiC 1304610 c.1680C>T synonymous_variant 0.43
fbiC 1304613 c.1683T>C synonymous_variant 0.15
fbiC 1304829 c.1899T>C synonymous_variant 0.21
fbiC 1304832 c.1902C>T synonymous_variant 0.21
fbiC 1304856 c.1926C>G synonymous_variant 0.4
fbiC 1304862 c.1932G>A synonymous_variant 0.17
fbiC 1304869 c.1939C>T synonymous_variant 0.18
fbiC 1304875 p.Ile649Val missense_variant 0.17
fbiC 1304883 p.Glu651Asp missense_variant 0.15
fbiC 1304891 p.Ile654Thr missense_variant 0.14
fbiC 1304893 p.Gly655Ser missense_variant 0.14
fbiC 1304928 c.1998T>C synonymous_variant 0.12
fbiC 1304937 c.2007G>C synonymous_variant 0.13
fbiC 1304958 c.2028T>G synonymous_variant 0.17
embR 1417019 p.Cys110Tyr missense_variant 0.24
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.12
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.13
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.17
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.25
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.25
rrl 1475202 n.1545G>C non_coding_transcript_exon_variant 0.15
rrl 1475443 n.1786G>A non_coding_transcript_exon_variant 0.14
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.19
rrl 1475475 n.1818C>T non_coding_transcript_exon_variant 0.23
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.23
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.23
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.27
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.27
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.22
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.13
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.22
rrl 1476117 n.2460G>C non_coding_transcript_exon_variant 0.19
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.14
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.23
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17
inhA 1674903 c.702T>C synonymous_variant 0.16
inhA 1674904 p.Ala235Pro missense_variant 0.15
inhA 1674942 c.741T>G synonymous_variant 0.13
rpsA 1833856 c.315A>G synonymous_variant 0.15
rpsA 1833886 c.345C>G synonymous_variant 0.15
rpsA 1833928 c.387G>C synonymous_variant 0.13
rpsA 1833970 c.429G>C synonymous_variant 0.13
rpsA 1833979 c.438T>C synonymous_variant 0.18
rpsA 1833991 c.450C>G synonymous_variant 0.13
rpsA 1834000 c.459G>C synonymous_variant 0.2
rpsA 1834021 c.480C>T synonymous_variant 0.19
rpsA 1834030 c.489C>G synonymous_variant 0.21
rpsA 1834081 c.540C>T synonymous_variant 0.14
rpsA 1834348 c.807T>C synonymous_variant 0.2
rpsA 1834366 c.825A>G synonymous_variant 0.2
rpsA 1834639 c.1098T>C synonymous_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 0.14
PPE35 2167926 p.Leu896Ser missense_variant 0.3
PPE35 2167983 p.Gly877Asp missense_variant 0.23
Rv1979c 2222308 p.Asp286Gly missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518076 c.-39C>T upstream_gene_variant 0.22
kasA 2518132 c.18C>T synonymous_variant 0.33
kasA 2518190 p.Ser26Ala missense_variant 0.13
kasA 2518199 p.Ile29Val missense_variant 0.16
kasA 2519062 c.948T>G synonymous_variant 0.17
ahpC 2726051 c.-142G>A upstream_gene_variant 0.26
Rv2752c 3066376 c.-185C>T upstream_gene_variant 0.2
thyX 3067376 c.570G>A synonymous_variant 0.12
thyX 3067391 c.555G>C synonymous_variant 0.14
thyX 3067394 c.552G>C synonymous_variant 0.14
thyX 3067439 c.507A>G synonymous_variant 0.16
thyX 3067445 c.501C>G synonymous_variant 0.16
thyX 3067457 c.489C>G synonymous_variant 0.14
thyX 3067465 p.Ile161Val missense_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.27
fprA 3475159 p.Asn385Asp missense_variant 0.2
rpoA 3877553 p.Glu319Gln missense_variant 0.14
rpoA 3877571 p.Pro313Ala missense_variant 0.14
rpoA 3877587 c.921A>G synonymous_variant 0.16
rpoA 3877613 p.Ile299Val missense_variant 0.13
rpoA 3877656 c.852T>G synonymous_variant 0.17
rpoA 3877668 c.840A>G synonymous_variant 0.17
rpoA 3877686 c.822A>G synonymous_variant 0.16
rpoA 3877692 c.816G>C synonymous_variant 0.15
rpoA 3877743 c.765T>C synonymous_variant 0.15
rpoA 3877764 c.744C>G synonymous_variant 0.15
rpoA 3877770 c.738A>G synonymous_variant 0.17
rpoA 3877776 c.732T>C synonymous_variant 0.17
rpoA 3877782 c.726T>C synonymous_variant 0.18
rpoA 3877818 c.690A>G synonymous_variant 0.19
rpoA 3877905 c.603A>G synonymous_variant 0.14
rpoA 3878271 c.237T>C synonymous_variant 0.18
rpoA 3878284 p.Glu75Ala missense_variant 0.14
rpoA 3878292 c.216T>C synonymous_variant 0.16
rpoA 3878313 c.195G>C synonymous_variant 0.15
clpC1 4038782 c.1923G>C synonymous_variant 0.17
clpC1 4038812 c.1893T>C synonymous_variant 0.19
clpC1 4038821 c.1884G>A synonymous_variant 0.13
clpC1 4038845 c.1860G>C synonymous_variant 0.15
clpC1 4038860 c.1845G>C synonymous_variant 0.14
clpC1 4038878 c.1827A>G synonymous_variant 0.13
clpC1 4038989 c.1716T>C synonymous_variant 0.14
clpC1 4038997 c.1708T>C synonymous_variant 0.15
clpC1 4039339 p.Thr456Pro missense_variant 0.13
clpC1 4039517 c.1188C>G synonymous_variant 0.14
clpC1 4039556 c.1149G>C synonymous_variant 0.13
clpC1 4039559 c.1146C>G synonymous_variant 0.13
clpC1 4039562 c.1143C>G synonymous_variant 0.14
clpC1 4039565 c.1140G>C synonymous_variant 0.14
clpC1 4039570 p.Met379Leu missense_variant 0.14
clpC1 4039577 c.1128T>C synonymous_variant 0.13
clpC1 4039589 c.1116G>C synonymous_variant 0.19
clpC1 4039616 c.1089G>C synonymous_variant 0.19
clpC1 4039622 c.1083C>T synonymous_variant 0.2
clpC1 4039649 c.1056G>T synonymous_variant 0.16
clpC1 4039652 c.1053G>T synonymous_variant 0.18
clpC1 4039664 c.1041G>C synonymous_variant 0.15
clpC1 4039682 c.1023C>G synonymous_variant 0.16
clpC1 4039694 c.1011G>C synonymous_variant 0.29
clpC1 4039724 c.981A>G synonymous_variant 0.23
clpC1 4039751 c.954A>G synonymous_variant 0.16
clpC1 4039757 c.948A>G synonymous_variant 0.13
clpC1 4039778 c.927A>G synonymous_variant 0.15
clpC1 4039781 c.924G>C synonymous_variant 0.12
clpC1 4039820 c.885T>G synonymous_variant 0.13
clpC1 4039826 c.879C>G synonymous_variant 0.13
clpC1 4039831 c.874T>C synonymous_variant 0.15
clpC1 4039850 c.855T>C synonymous_variant 0.14
clpC1 4039865 c.840T>C synonymous_variant 0.16
clpC1 4039898 c.807C>G synonymous_variant 0.16
clpC1 4039928 p.Ser259Trp missense_variant 0.13
clpC1 4039931 c.774T>C synonymous_variant 0.16
clpC1 4039946 c.759A>C synonymous_variant 0.15
clpC1 4039952 c.753T>C synonymous_variant 0.17
clpC1 4040021 c.684A>C synonymous_variant 0.15
clpC1 4040024 c.681A>G synonymous_variant 0.17
clpC1 4040033 c.672G>C synonymous_variant 0.15
clpC1 4040459 c.246C>G synonymous_variant 0.15
clpC1 4040471 c.234T>C synonymous_variant 0.13
clpC1 4040477 c.228G>C synonymous_variant 0.14
clpC1 4040480 c.225T>G synonymous_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 0.13
embC 4240671 p.Thr270Ile missense_variant 0.27
embC 4241042 p.Asn394Asp missense_variant 0.4
embC 4241530 c.1668C>A synonymous_variant 0.13
embC 4241648 c.1786_1788delTTGinsCTC synonymous_variant 0.12
embC 4241657 p.Ser599Pro missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.61
embA 4243848 p.Val206Met missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 0.27
embB 4247050 c.537C>T synonymous_variant 0.27
embB 4247356 c.843C>T synonymous_variant 0.24
embB 4247646 p.Glu378Ala missense_variant 0.32
aftB 4268683 p.Gly52Ser missense_variant 0.49
aftB 4269006 c.-170T>C upstream_gene_variant 0.12
aftB 4269042 c.-206G>C upstream_gene_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 0.25
aftB 4269606 c.-770T>C upstream_gene_variant 0.33
whiB6 4338441 p.Tyr27* stop_gained 0.22
whiB6 4338449 p.Ala25Pro missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 0.27
gid 4407588 c.615A>G synonymous_variant 0.26
gid 4407873 c.330G>T synonymous_variant 0.21