TB-Profiler result

Run: ERR7801220
Summary

Run ID: ERR7801220

Sample name:

Date: 02-04-2023 05:59:19

Number of reads: 905257

Percentage reads mapped: 99.45

Strain: lineage4.3.4.2.1

Drug-resistance: HR-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 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 1.0
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 0.99
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
katG 2154309 c.1802dupG frameshift_variant 0.11 isoniazid
katG 2155515 c.596dupG frameshift_variant 0.14 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
gyrB 5609 p.Gly124Cys missense_variant 0.17
gyrB 5754 p.Arg172Leu missense_variant 0.14
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrB 7087 p.Met616Ile missense_variant 0.13
gyrB 7104 p.Trp622Leu missense_variant 0.15
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7716 p.Met139Leu missense_variant 0.11
gyrA 7831 p.Gly177Val missense_variant 0.12
gyrA 7868 c.567C>A synonymous_variant 0.14
gyrA 7901 c.600G>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575187 c.-161G>C upstream_gene_variant 0.14
mshA 575378 p.Gly11Trp missense_variant 0.13
mshA 575433 c.89delC frameshift_variant 0.11
mshA 575440 c.96dupG frameshift_variant 0.11
mshA 576567 p.Arg407Leu missense_variant 0.18
ccsA 619847 c.-44C>A upstream_gene_variant 0.14
ccsA 620198 p.Gln103Arg missense_variant 0.12
ccsA 620267 p.Ala126Val missense_variant 0.12
ccsA 620604 c.714C>A synonymous_variant 0.15
rpoB 759685 c.-122C>T upstream_gene_variant 0.15
rpoB 760682 p.Asn292Lys missense_variant 0.12
rpoB 760731 p.Lys309Glu missense_variant 0.13
rpoB 762657 p.Ala951Thr missense_variant 0.15
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 766796 p.Arg1143Ser missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775941 p.Gly847Val missense_variant 0.11
mmpL5 777542 c.939G>T synonymous_variant 0.18
mmpL5 777570 p.Gly304Val missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304030 p.Pro367His missense_variant 0.17
fbiC 1305120 p.Gln730His missense_variant 0.13
Rv1258c 1406943 c.397_398insGC frameshift_variant 0.11
Rv1258c 1406946 p.Ala132Gly missense_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473205 n.1360T>C non_coding_transcript_exon_variant 0.1
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.15
rrl 1473967 n.310G>T non_coding_transcript_exon_variant 0.4
fabG1 1674158 p.Asp240Gly missense_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-132delG upstream_gene_variant 0.11
katG 2154407 p.Pro569Thr missense_variant 0.21
katG 2154846 c.1266C>A synonymous_variant 0.18
PPE35 2169432 p.Pro394Gln missense_variant 0.14
PPE35 2169895 p.Gly240Cys missense_variant 0.15
PPE35 2169906 c.705_706delCA frameshift_variant 0.17
PPE35 2170349 c.264C>A synonymous_variant 0.17
Rv1979c 2221925 p.Asp414Asn missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288770 p.Asp158Tyr missense_variant 0.13
pncA 2288909 p.Glu111Asp missense_variant 0.15
kasA 2518052 c.-63G>T upstream_gene_variant 0.16
kasA 2518503 p.Asn130Thr missense_variant 0.11
kasA 2518536 p.Ala141Asp missense_variant 0.12
folC 2747369 p.Ser77Leu missense_variant 0.14
Rv2752c 3064577 p.Lys539Glu missense_variant 0.18
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087796 p.Asp326Gly missense_variant 0.1
ald 3087903 p.Pro362Ser missense_variant 0.11
fbiD 3339593 p.His159Arg missense_variant 0.11
fbiD 3339732 c.615C>T synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474180 c.174C>A synonymous_variant 0.13
fprA 3474329 p.Ser108Tyr missense_variant 0.14
fprA 3474420 c.414C>T synonymous_variant 0.14
fprA 3474778 p.Arg258Cys missense_variant 0.18
fprA 3475234 p.Leu410Ile missense_variant 0.12
whiB7 3568633 p.Pro16Gln missense_variant 0.17
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612228 p.Leu297Met missense_variant 0.14
Rv3236c 3612232 c.885G>T synonymous_variant 0.13
Rv3236c 3613127 c.-11G>T upstream_gene_variant 0.12
fbiB 3640641 c.-894C>A upstream_gene_variant 0.18
fbiA 3640657 p.His39Asn missense_variant 0.18
fbiA 3640721 p.Pro60Gln missense_variant 0.25
fbiB 3641196 c.-339C>A upstream_gene_variant 0.22
fbiA 3641389 p.Gly283Trp missense_variant 0.14
fbiB 3641457 c.-78G>T upstream_gene_variant 0.15
fbiB 3641538 c.6dupC frameshift_variant 0.17
fbiB 3641646 p.Pro38Thr missense_variant 0.12
fbiB 3642201 p.Ser223Pro missense_variant 0.13
fbiB 3642708 p.Gly392Trp missense_variant 0.19
alr 3840719 c.702A>G synonymous_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4038724 c.1980delC frameshift_variant 0.17
clpC1 4040013 c.691delC frameshift_variant 0.2
clpC1 4040078 p.Lys209Asn missense_variant 0.17
embC 4241075 p.Gly405Cys missense_variant 0.13
embC 4241137 c.1275G>T synonymous_variant 0.13
embC 4241168 p.Leu436Met missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244489 c.1257G>T synonymous_variant 0.18
embA 4244753 c.1521G>T synonymous_variant 0.14
embB 4247825 p.Ala438Ser missense_variant 0.2
embB 4249287 p.Gln925Arg missense_variant 0.15
embB 4249291 c.2778C>A synonymous_variant 0.21
embB 4249720 c.3207C>A synonymous_variant 0.29
aftB 4268730 p.Arg36Leu missense_variant 0.15
ubiA 4268944 c.889delG frameshift_variant 0.11
whiB6 4338302 p.Gly74Trp missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0