TB-Profiler result

Run: SRR22528569
Summary

Run ID: SRR22528569

Sample name:

Date: 04-04-2023 04:18:58

Number of reads: 282572

Percentage reads mapped: 99.64

Strain: lineage4.1.1

Drug-resistance: Pre-XDR-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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
gyrB 6620 p.Asp461Asn missense_variant 0.25 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2154344 c.1767delC frameshift_variant 0.33 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 5736 p.Lys166Met missense_variant 0.25
gyrB 5858 p.Asn207Asp missense_variant 1.0
gyrB 7140 p.Arg634Pro missense_variant 0.29
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7584 c.283_284delAGinsTC synonymous_variant 0.29
gyrA 7639 c.341delG frameshift_variant 0.2
gyrA 7913 c.612G>A synonymous_variant 0.33
gyrA 8439 p.Arg380Trp missense_variant 0.2
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9382 p.Gly694Val missense_variant 0.22
gyrA 9656 c.2355C>T synonymous_variant 0.14
fgd1 491236 p.Gly152Ser missense_variant 0.14
mshA 575899 c.552G>A synonymous_variant 0.15
ccsA 620409 c.519C>T synonymous_variant 0.29
rpoB 760962 p.Gly386Ser missense_variant 0.2
rpoB 761652 p.Glu616Lys missense_variant 0.17
rpoB 762601 p.Trp932Leu missense_variant 0.18
rpoC 764961 p.Ala531Val missense_variant 0.15
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766306 c.2940delG frameshift_variant 0.22
rpoC 766714 c.3345G>A synonymous_variant 0.17
rpoC 767180 p.Ala1271Ser missense_variant 0.2
rpoC 767310 p.Asp1314Val missense_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776103 p.Ile793Asn missense_variant 0.33
mmpL5 777155 c.1326G>T synonymous_variant 0.27
mmpL5 777412 p.Ile357Leu missense_variant 0.18
mmpL5 777915 p.Ser189Leu missense_variant 0.2
mmpL5 777944 c.537A>T synonymous_variant 0.22
mmpL5 778062 p.Gln140Leu missense_variant 0.2
mmpL5 778074 p.Ala136Gly missense_variant 0.22
mmpR5 778202 c.-788G>A upstream_gene_variant 0.2
mmpS5 778524 p.Ala128Ser missense_variant 0.17
mmpS5 778821 p.Arg29Cys missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781514 c.-46G>A upstream_gene_variant 0.15
rpsL 781920 p.Lys121Glu missense_variant 0.13
rplC 800694 c.-115C>T upstream_gene_variant 0.2
fbiC 1302738 c.-193G>A upstream_gene_variant 0.14
fbiC 1305408 c.2478G>T synonymous_variant 0.2
Rv1258c 1406136 c.1203_1204delCG frameshift_variant 0.2
embR 1416574 p.Gln258His missense_variant 0.2
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473399 n.-259A>T upstream_gene_variant 0.29
rrl 1473417 n.-241C>A upstream_gene_variant 0.29
rrl 1473904 n.247G>A non_coding_transcript_exon_variant 0.25
rrl 1474520 n.863A>G non_coding_transcript_exon_variant 0.67
fabG1 1673572 p.Thr45Ala missense_variant 0.12
rpsA 1834898 p.Ser453Cys missense_variant 0.17
tlyA 1917792 c.-148G>A upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918539 c.600C>T synonymous_variant 0.17
katG 2154400 p.Arg571His missense_variant 0.25
katG 2154837 p.Arg425Ser missense_variant 0.22
PPE35 2168636 c.1977G>A synonymous_variant 0.4
PPE35 2168791 p.Pro608Thr missense_variant 0.4
PPE35 2169475 p.Gly380Ser missense_variant 0.67
PPE35 2170074 p.Ala180Val missense_variant 0.33
Rv1979c 2222677 p.Asn163Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290113 c.-872G>A upstream_gene_variant 1.0
kasA 2518095 c.-20A>T upstream_gene_variant 0.18
eis 2714552 p.Ser261Thr missense_variant 0.13
eis 2714633 p.Lys234Glu missense_variant 0.15
eis 2715186 c.147C>T synonymous_variant 0.18
eis 2715331 p.Val1Glu missense_variant 0.18
eis 2715491 c.-159G>A upstream_gene_variant 0.13
folC 2746552 c.1047C>T synonymous_variant 0.15
pepQ 2860077 c.342G>A synonymous_variant 1.0
ribD 2987553 p.Arg239Cys missense_variant 1.0
Rv2752c 3064854 c.1338G>A synonymous_variant 0.17
Rv2752c 3067150 c.-959T>A upstream_gene_variant 0.22
thyA 3074104 p.Pro123Leu missense_variant 0.14
thyA 3074353 p.Ala40Val missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087822 p.Ser335Thr missense_variant 0.15
ald 3087875 c.1056C>T synonymous_variant 0.17
Rv3083 3449339 p.Arg279His missense_variant 0.14
Rv3083 3449364 c.861C>G synonymous_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568841 c.-162T>A upstream_gene_variant 0.17
Rv3236c 3612370 c.747C>T synonymous_variant 0.14
Rv3236c 3612674 c.442delA frameshift_variant 0.29
Rv3236c 3612692 p.Arg142Gln missense_variant 0.33
Rv3236c 3612802 c.314delC frameshift_variant 0.29
Rv3236c 3612896 p.Gly74Val missense_variant 0.4
fbiA 3640396 c.-147T>A upstream_gene_variant 0.5
fbiA 3640449 c.-94T>A upstream_gene_variant 0.5
fbiB 3641388 c.-147C>T upstream_gene_variant 0.4
fbiB 3642370 p.Ala279Val missense_variant 0.15
fbiB 3642399 p.Pro289Ser missense_variant 0.17
alr 3840244 p.Ser393Gly missense_variant 0.18
alr 3841271 c.150G>A synonymous_variant 0.22
alr 3841313 c.108C>T synonymous_variant 0.2
rpoA 3878009 c.498delC frameshift_variant 0.5
rpoA 3878030 p.Gly160Arg missense_variant 0.33
rpoA 3878629 c.-122A>C upstream_gene_variant 0.33
ddn 3987024 p.Val61Phe missense_variant 0.18
ddn 3987274 p.Ile144Thr missense_variant 0.2
clpC1 4040158 p.Met183Leu missense_variant 0.25
clpC1 4040165 c.540G>T synonymous_variant 0.25
clpC1 4040213 c.492T>A synonymous_variant 0.18
embC 4240086 p.Ile75Thr missense_variant 0.13
embC 4240284 p.Thr141Ile missense_variant 0.17
embC 4240353 p.Val164Asp missense_variant 0.25
embC 4240489 c.627A>G synonymous_variant 0.22
embC 4240498 c.636G>T synonymous_variant 0.22
embC 4240545 p.Pro228Leu missense_variant 0.22
embC 4240686 p.Thr275Asn missense_variant 0.17
embC 4241262 p.Phe467Tyr missense_variant 0.25
embC 4241769 p.Ser636Ile missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4245160 p.Ser643Ile missense_variant 0.18
embB 4246160 c.-354G>T upstream_gene_variant 0.18
embB 4248155 c.1642C>T synonymous_variant 0.2
embB 4248246 p.Ile578Thr missense_variant 0.29
embB 4249408 c.2895G>A synonymous_variant 1.0
aftB 4268113 p.Ala242Thr missense_variant 0.14
aftB 4268175 p.Pro221Arg missense_variant 0.15
aftB 4268618 c.219G>A synonymous_variant 0.2
aftB 4268704 p.Asn45Asp missense_variant 0.11
aftB 4269072 c.-236G>A upstream_gene_variant 0.15
ubiA 4269917 c.-84G>T upstream_gene_variant 0.14
ethR 4327827 p.Asn93Lys missense_variant 0.14
whiB6 4338585 c.-64G>A upstream_gene_variant 0.29
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407809 p.Asp132Asn missense_variant 0.2
gid 4407946 p.Leu86His missense_variant 1.0