TB-Profiler result

Run: SRR11349186
Summary

Run ID: SRR11349186

Sample name:

Date: 02-04-2023 20:55:05

Number of reads: 3981696

Percentage reads mapped: 82.39

Strain: lineage4.3.3

Drug-resistance: MDR-TB

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 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 761155 p.Ser450Leu missense_variant 0.93 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.84 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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 6727 c.-575G>T upstream_gene_variant 0.12
gyrA 6728 c.-574C>T upstream_gene_variant 0.12
gyrA 6760 c.-542G>C upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7475 c.174A>G synonymous_variant 0.11
gyrA 7484 c.183T>C synonymous_variant 0.13
gyrA 7490 c.189C>G synonymous_variant 0.13
gyrA 7496 c.195C>G synonymous_variant 0.14
gyrA 7499 c.198G>C synonymous_variant 0.15
gyrA 7523 c.222C>G synonymous_variant 0.16
gyrA 7526 c.225G>C synonymous_variant 0.16
gyrA 7532 c.231T>G synonymous_variant 0.15
gyrA 7559 c.258G>A synonymous_variant 0.12
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8040 p.Gly247Ser missense_variant 1.0
gyrA 8990 c.1689C>G synonymous_variant 0.12
gyrA 8993 c.1692C>T synonymous_variant 0.13
gyrA 8996 c.1695T>C synonymous_variant 0.13
gyrA 8998 p.Leu566Trp missense_variant 0.13
gyrA 9018 p.Gln573Lys missense_variant 0.15
gyrA 9026 c.1725G>C synonymous_variant 0.14
gyrA 9029 c.1728T>C synonymous_variant 0.13
gyrA 9032 c.1731T>C synonymous_variant 0.13
gyrA 9035 c.1734G>C synonymous_variant 0.13
gyrA 9044 c.1743C>G synonymous_variant 0.13
gyrA 9051 c.1750T>C synonymous_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575909 p.Leu188Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.35
rpoB 760184 c.378A>G synonymous_variant 0.13
rpoB 760196 c.390C>G synonymous_variant 0.12
rpoB 760223 c.417T>C synonymous_variant 0.14
rpoB 760235 c.429T>C synonymous_variant 0.14
rpoB 760244 c.438G>C synonymous_variant 0.14
rpoB 761051 c.1245G>T synonymous_variant 0.15
rpoB 761054 c.1248G>C synonymous_variant 0.14
rpoB 761057 c.1251G>C synonymous_variant 0.14
rpoB 761060 c.1254C>G synonymous_variant 0.14
rpoB 761063 c.1257C>G synonymous_variant 0.15
rpoB 761084 c.1278C>A synonymous_variant 0.16
rpoB 761097 c.1291_1293delAGCinsTCG synonymous_variant 0.13
rpoB 761102 c.1296A>G synonymous_variant 0.13
rpoB 761615 c.1809A>C synonymous_variant 0.12
rpoB 761645 c.1839C>G synonymous_variant 0.12
rpoB 761648 c.1842T>C synonymous_variant 0.12
rpoB 761693 c.1887G>C synonymous_variant 0.11
rpoB 761955 p.Ile717Val missense_variant 0.14
rpoB 761969 c.2163G>A synonymous_variant 0.18
rpoB 761990 c.2184G>C synonymous_variant 0.18
rpoB 762008 c.2202C>T synonymous_variant 0.16
rpoB 762014 c.2208C>G synonymous_variant 0.17
rpoB 762038 c.2232C>T synonymous_variant 0.13
rpoB 762047 c.2241G>A synonymous_variant 0.12
rpoB 762065 c.2259T>G synonymous_variant 0.14
rpoB 762083 c.2277T>C synonymous_variant 0.11
rpoB 762167 c.2361T>C synonymous_variant 0.11
rpoB 762176 c.2370T>C synonymous_variant 0.14
rpoB 762185 c.2379G>C synonymous_variant 0.15
rpoB 762194 c.2388G>C synonymous_variant 0.16
rpoB 762221 c.2415G>A synonymous_variant 0.13
rpoB 762233 c.2427G>C synonymous_variant 0.13
rpoB 762236 c.2430G>C synonymous_variant 0.13
rpoB 762245 c.2439G>C synonymous_variant 0.13
rpoC 762920 c.-450C>T upstream_gene_variant 0.12
rpoC 762923 c.-447C>G upstream_gene_variant 0.12
rpoC 762959 c.-411G>C upstream_gene_variant 0.17
rpoC 762962 c.-408C>T upstream_gene_variant 0.16
rpoC 762983 c.-387C>T upstream_gene_variant 0.2
rpoC 762989 c.-381G>A upstream_gene_variant 0.19
rpoC 762995 c.-375G>T upstream_gene_variant 0.18
rpoC 763031 c.-339T>G upstream_gene_variant 0.21
rpoC 763034 c.-336C>A upstream_gene_variant 0.2
rpoC 763040 c.-330C>G upstream_gene_variant 0.21
rpoC 763070 c.-300T>C upstream_gene_variant 0.24
rpoC 763082 c.-288C>T upstream_gene_variant 0.22
rpoC 763085 c.-285C>T upstream_gene_variant 0.22
rpoC 763088 c.-282C>G upstream_gene_variant 0.21
rpoC 763094 c.-276G>C upstream_gene_variant 0.21
rpoC 763115 c.-255T>C upstream_gene_variant 0.2
rpoC 763127 c.-243G>C upstream_gene_variant 0.2
rpoC 763136 c.-234C>T upstream_gene_variant 0.18
rpoC 763142 c.-228C>G upstream_gene_variant 0.19
rpoC 763570 c.201G>C synonymous_variant 0.13
rpoC 764566 c.1197C>G synonymous_variant 0.13
rpoC 764575 c.1206T>G synonymous_variant 0.14
rpoC 764578 c.1209C>G synonymous_variant 0.15
rpoC 764593 c.1224C>T synonymous_variant 0.13
rpoC 764626 c.1257C>T synonymous_variant 0.13
rpoC 764713 c.1344G>T synonymous_variant 0.15
rpoC 764746 c.1377G>T synonymous_variant 0.17
rpoC 764752 c.1383G>C synonymous_variant 0.16
rpoC 764758 c.1389C>G synonymous_variant 0.18
rpoC 764764 c.1395T>C synonymous_variant 0.18
rpoC 764803 c.1434C>T synonymous_variant 0.15
rpoC 764810 p.Pro481Ala missense_variant 0.16
rpoC 764815 c.1446A>G synonymous_variant 0.16
rpoC 764827 c.1458G>C synonymous_variant 0.15
rpoC 764858 c.1489T>C synonymous_variant 0.15
rpoC 764869 c.1500C>T synonymous_variant 0.13
rpoC 764875 c.1506C>A synonymous_variant 0.14
rpoC 764878 c.1509C>G synonymous_variant 0.13
rpoC 764887 c.1518G>C synonymous_variant 0.13
rpoC 764888 c.1519T>C synonymous_variant 0.13
rpoC 764932 c.1563C>A synonymous_variant 0.12
rpoC 764948 c.1579T>C synonymous_variant 0.12
rpoC 764968 c.1599T>C synonymous_variant 0.14
rpoC 764995 c.1626C>G synonymous_variant 0.87
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 778346 c.-644G>A upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.13
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.15
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.17
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.18
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.22
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.23
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.19
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.2
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.19
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.19
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.19
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.18
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.16
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.12
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.13
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.13
rrs 1473129 n.1284C>T non_coding_transcript_exon_variant 0.13
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.15
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.17
rrs 1473288 n.1443C>T non_coding_transcript_exon_variant 0.17
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.16
rrs 1473291 n.1446G>T non_coding_transcript_exon_variant 0.16
rrl 1473815 n.158T>G non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.14
rrl 1474263 n.606G>A non_coding_transcript_exon_variant 0.16
rrl 1474282 n.625G>A non_coding_transcript_exon_variant 0.14
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.14
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.15
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.13
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.13
rrl 1474376 n.719T>A non_coding_transcript_exon_variant 0.13
rrl 1474496 n.839C>G non_coding_transcript_exon_variant 0.13
rrl 1474497 n.840G>C non_coding_transcript_exon_variant 0.14
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.14
rrl 1474507 n.850G>C non_coding_transcript_exon_variant 0.13
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.14
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.17
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.17
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.18
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.12
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.13
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.11
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.18
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.22
rrl 1476295 n.2638C>T non_coding_transcript_exon_variant 0.21
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.22
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.22
rrl 1476311 n.2654G>A non_coding_transcript_exon_variant 0.22
rpsA 1833604 c.63C>T synonymous_variant 0.12
rpsA 1833619 c.78A>C synonymous_variant 0.13
rpsA 1833625 c.84A>G synonymous_variant 0.13
rpsA 1833661 c.120A>G synonymous_variant 0.16
rpsA 1833664 c.123C>G synonymous_variant 0.15
rpsA 1833685 c.144G>C synonymous_variant 0.12
rpsA 1833734 p.Ala65Ser missense_variant 0.12
rpsA 1833748 c.207C>G synonymous_variant 0.12
rpsA 1833760 c.219C>T synonymous_variant 0.14
rpsA 1833787 c.246C>G synonymous_variant 0.16
rpsA 1833790 c.249T>C synonymous_variant 0.15
rpsA 1833802 c.261A>G synonymous_variant 0.14
rpsA 1833829 c.288A>G synonymous_variant 0.13
rpsA 1833832 c.291G>A synonymous_variant 0.13
rpsA 1833838 c.297G>T synonymous_variant 0.14
rpsA 1833841 c.300C>G synonymous_variant 0.14
rpsA 1833847 c.306C>G synonymous_variant 0.13
rpsA 1833856 c.315A>G synonymous_variant 0.14
rpsA 1833862 c.321G>T synonymous_variant 0.14
rpsA 1833874 c.333T>G synonymous_variant 0.13
rpsA 1833886 c.345C>G synonymous_variant 0.13
rpsA 1833892 c.351G>A synonymous_variant 0.12
rpsA 1833928 c.387G>C synonymous_variant 0.15
rpsA 1833949 c.408T>C synonymous_variant 0.15
rpsA 1833970 c.429G>C synonymous_variant 0.17
rpsA 1833979 c.438T>C synonymous_variant 0.15
rpsA 1833991 c.450C>G synonymous_variant 0.15
rpsA 1834000 c.459G>C synonymous_variant 0.15
rpsA 1834015 c.474G>C synonymous_variant 0.11
rpsA 1834021 c.480C>T synonymous_variant 0.12
rpsA 1834261 c.720A>G synonymous_variant 0.12
rpsA 1834264 c.723G>C synonymous_variant 0.12
rpsA 1834297 c.756C>T synonymous_variant 0.13
rpsA 1834306 c.765T>C synonymous_variant 0.13
rpsA 1834339 c.798C>T synonymous_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.12
rpsA 1834366 c.825A>G synonymous_variant 0.12
rpsA 1834423 c.882G>C synonymous_variant 0.11
rpsA 1834435 c.894G>C synonymous_variant 0.15
rpsA 1834451 c.910T>C synonymous_variant 0.17
rpsA 1834456 c.915T>G synonymous_variant 0.18
rpsA 1834468 c.927A>G synonymous_variant 0.17
rpsA 1834480 c.939C>G synonymous_variant 0.18
rpsA 1834483 c.942G>A synonymous_variant 0.18
rpsA 1834489 c.948T>C synonymous_variant 0.19
rpsA 1834498 c.957C>T synonymous_variant 0.19
rpsA 1834520 p.Ala327Ser missense_variant 0.15
rpsA 1834528 c.987T>C synonymous_variant 0.19
rpsA 1834543 c.1002C>G synonymous_variant 0.19
rpsA 1834552 c.1011G>T synonymous_variant 0.17
rpsA 1834555 c.1014T>G synonymous_variant 0.17
rpsA 1834557 p.Ala339Gly missense_variant 0.16
rpsA 1834606 c.1065C>T synonymous_variant 0.14
rpsA 1834609 c.1068T>C synonymous_variant 0.14
rpsA 1834612 c.1071G>C synonymous_variant 0.14
rpsA 1834619 c.1078T>C synonymous_variant 0.13
rpsA 1834622 c.1081_1083delTCGinsAGC synonymous_variant 0.13
rpsA 1834633 c.1092A>G synonymous_variant 0.14
rpsA 1834639 c.1098T>C synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289208 p.Asp12Tyr missense_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2747225 p.Arg125Gln missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878160 c.348C>G synonymous_variant 0.11
rpoA 3878169 c.339G>C synonymous_variant 0.11
rpoA 3878184 c.324C>T synonymous_variant 0.12
rpoA 3878217 c.291A>G synonymous_variant 0.12
rpoA 3878259 c.249G>C synonymous_variant 0.12
rpoA 3878298 c.210A>G synonymous_variant 0.14
rpoA 3878301 c.207C>G synonymous_variant 0.12
rpoA 3878310 c.198G>T synonymous_variant 0.12
rpoA 3878313 c.195G>C synonymous_variant 0.12
rpoA 3878322 c.186A>G synonymous_variant 0.13
rpoA 3878331 c.177A>G synonymous_variant 0.13
rpoA 3878334 c.174T>C synonymous_variant 0.13
rpoA 3878337 c.171T>C synonymous_variant 0.13
rpoA 3878364 c.144A>C synonymous_variant 0.12
rpoA 3878618 c.-111A>C upstream_gene_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4039694 c.1011G>C synonymous_variant 0.14
clpC1 4039724 c.981A>G synonymous_variant 0.14
clpC1 4039733 c.972G>C synonymous_variant 0.13
clpC1 4039739 c.966C>G synonymous_variant 0.13
clpC1 4039751 c.954A>G synonymous_variant 0.17
clpC1 4039757 c.948A>G synonymous_variant 0.18
clpC1 4039769 c.936C>T synonymous_variant 0.17
clpC1 4039775 c.930G>C synonymous_variant 0.17
clpC1 4039778 c.927A>G synonymous_variant 0.17
clpC1 4039793 c.912C>G synonymous_variant 0.17
clpC1 4039805 c.900C>T synonymous_variant 0.18
clpC1 4039814 c.891C>G synonymous_variant 0.17
clpC1 4039817 c.888A>C synonymous_variant 0.18
clpC1 4039820 c.885T>G synonymous_variant 0.18
clpC1 4039831 c.874T>C synonymous_variant 0.17
clpC1 4039850 c.855T>C synonymous_variant 0.16
clpC1 4039865 c.840T>C synonymous_variant 0.14
clpC1 4039907 c.798G>A synonymous_variant 0.14
clpC1 4039931 c.774T>C synonymous_variant 0.12
clpC1 4039934 c.771G>C synonymous_variant 0.12
clpC1 4039943 c.762G>C synonymous_variant 0.13
clpC1 4039946 c.759A>G synonymous_variant 0.13
clpC1 4039949 c.756G>C synonymous_variant 0.13
clpC1 4039952 c.753T>C synonymous_variant 0.13
clpC1 4039958 c.747G>C synonymous_variant 0.13
clpC1 4039964 c.741C>G synonymous_variant 0.15
clpC1 4039975 p.Asp244Asn missense_variant 0.17
clpC1 4039979 c.726C>G synonymous_variant 0.17
clpC1 4039982 c.723G>A synonymous_variant 0.16
clpC1 4040000 c.705C>T synonymous_variant 0.15
clpC1 4040021 c.684A>C synonymous_variant 0.16
clpC1 4040024 c.681A>G synonymous_variant 0.15
clpC1 4040033 c.672G>C synonymous_variant 0.13
clpC1 4040042 c.663C>T synonymous_variant 0.14
clpC1 4040057 c.648C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338367 p.Leu52Gln missense_variant 1.0
whiB6 4338593 c.-73delT upstream_gene_variant 1.0
whiB6 4338596 c.-75G>C upstream_gene_variant 1.0
gid 4407986 p.Gly73Arg missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0