TB-Profiler result

Run: SRR4035801
Summary

Run ID: SRR4035801

Sample name:

Date: 04-04-2023 07:18:27

Number of reads: 1643750

Percentage reads mapped: 99.38

Strain: lineage4.1.2

Drug-resistance: Other

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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 0.99
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.2 Euro-American T;H None 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
gid 4408137 p.Tyr22* stop_gained 0.12 streptomycin
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 5470 c.231C>T synonymous_variant 0.13
gyrB 5520 p.Pro94Arg missense_variant 0.18
gyrA 7318 p.Leu6* stop_gained 0.14
gyrA 7327 p.Asp9Gly missense_variant 0.12
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7717 p.Met139Thr missense_variant 0.11
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491278 p.Pro166Ser missense_variant 0.17
fgd1 491285 p.Gly168Val missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 0.94
mshA 575220 c.-128G>C upstream_gene_variant 0.11
mshA 575665 c.318G>C synonymous_variant 0.15
mshA 576389 p.Val348Leu missense_variant 0.15
mshA 576458 p.Ala371Pro missense_variant 0.15
mshA 576616 c.1269G>T synonymous_variant 0.15
mshA 576631 c.1284C>T synonymous_variant 0.17
ccsA 620376 c.486G>T synonymous_variant 0.17
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 761029 p.Pro408Arg missense_variant 0.11
rpoB 761538 p.Arg578Cys missense_variant 0.15
rpoC 763411 c.42T>C synonymous_variant 0.11
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 0.9
rpoC 767131 p.Ile1254Met missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 1.0
mmpR5 778001 c.-989T>C upstream_gene_variant 0.12
mmpL5 778120 p.Thr121Ala missense_variant 0.11
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303224 c.294C>T synonymous_variant 0.12
fbiC 1304433 c.1503G>C synonymous_variant 0.12
fbiC 1304439 p.Glu503Asp missense_variant 0.11
fbiC 1304526 c.1596T>C synonymous_variant 0.12
fbiC 1304537 p.Arg536Pro missense_variant 0.13
fbiC 1304551 p.Gly541Ser missense_variant 0.13
fbiC 1304823 p.His631Gln missense_variant 0.14
fbiC 1305079 p.Arg717Gly missense_variant 0.25
fbiC 1305088 p.Val720Leu missense_variant 0.25
fbiC 1305103 p.Val725Met missense_variant 0.17
Rv1258c 1406458 p.Val295Ile missense_variant 0.15
Rv1258c 1406979 c.358_361delGGCA frameshift_variant 0.18
Rv1258c 1407288 p.Met18Lys missense_variant 0.15
Rv1258c 1407304 p.Leu13Val missense_variant 0.13
embR 1416619 c.729C>A synonymous_variant 0.14
embR 1416628 c.720C>G synonymous_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474909 n.1252C>T non_coding_transcript_exon_variant 0.12
rrl 1474930 n.1273A>G non_coding_transcript_exon_variant 0.11
inhA 1674410 p.His70Arg missense_variant 0.11
rpsA 1833383 c.-159C>T upstream_gene_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917982 p.Gly15Ser missense_variant 0.14
tlyA 1918696 p.Ala253Ser missense_variant 0.12
ndh 2102154 p.Leu297Phe missense_variant 0.14
katG 2154432 c.1680C>G synonymous_variant 0.13
katG 2155481 p.Ser211Arg missense_variant 0.11
katG 2155970 p.Leu48Val missense_variant 0.12
katG 2155994 p.Pro40Ser missense_variant 0.17
katG 2156436 c.-325C>A upstream_gene_variant 0.16
PPE35 2169121 p.Val498Leu missense_variant 0.11
PPE35 2169182 c.1431G>A synonymous_variant 0.14
PPE35 2169443 c.1170T>C synonymous_variant 0.11
PPE35 2170352 c.261C>A synonymous_variant 0.18
PPE35 2170415 c.198A>T synonymous_variant 0.25
PPE35 2170483 p.Ser44Ala missense_variant 0.1
Rv1979c 2222545 p.Leu207Ser missense_variant 0.1
Rv1979c 2222659 p.Gly169Asp missense_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289447 c.-206G>C upstream_gene_variant 0.11
pncA 2289863 c.-623_-622delAGinsGA upstream_gene_variant 0.13
pncA 2290007 c.-766A>G upstream_gene_variant 0.11
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2519331 p.Gly406Asp missense_variant 0.15
folC 2746551 p.Ile350Val missense_variant 0.18
folC 2746578 p.Arg341Cys missense_variant 0.13
folC 2746611 p.Phe330Leu missense_variant 0.11
folC 2746707 p.Gln298* stop_gained 0.13
pepQ 2859879 p.Met180Ile missense_variant 0.13
pepQ 2860164 c.255C>G synonymous_variant 0.12
ribD 2986656 c.-183A>G upstream_gene_variant 0.11
ribD 2987336 c.498C>A synonymous_variant 0.15
ribD 2987569 p.Leu244His missense_variant 0.2
Rv2752c 3065598 c.594G>T synonymous_variant 0.12
thyX 3067288 p.Ala220Thr missense_variant 0.17
thyX 3067509 p.Leu146Gln missense_variant 0.13
thyX 3068040 c.-95C>A upstream_gene_variant 0.15
thyX 3068081 c.-136A>G upstream_gene_variant 0.15
thyA 3074404 p.Gly23Asp missense_variant 0.12
thyA 3074510 c.-39C>A upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087873 p.Ser352Pro missense_variant 0.13
Rv3083 3448704 c.201C>T synonymous_variant 0.12
Rv3083 3449405 p.Pro301Leu missense_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612021 p.Gly366Arg missense_variant 0.18
fbiA 3640546 p.Lys2Glu missense_variant 0.13
fbiA 3641116 p.Lys192Glu missense_variant 0.12
fbiA 3641129 p.Ala196Val missense_variant 0.2
fbiB 3641917 p.Ser128Thr missense_variant 0.17
fbiB 3642274 p.Glu247Gly missense_variant 0.12
alr 3841117 p.Ala102Thr missense_variant 0.17
alr 3841378 p.Thr15Ser missense_variant 0.14
alr 3841385 c.36C>T synonymous_variant 0.14
rpoA 3878092 p.Val139Ala missense_variant 0.12
ddn 3986933 c.90C>T synonymous_variant 0.13
ddn 3986977 p.Pro45Leu missense_variant 0.13
clpC1 4039242 p.Leu488Pro missense_variant 0.11
clpC1 4040235 p.Gly157Ala missense_variant 0.15
embC 4240223 c.361C>T synonymous_variant 0.14
embC 4240238 p.Ala126Thr missense_variant 0.13
embC 4241002 c.1140G>A synonymous_variant 0.13
embC 4241017 c.1155T>C synonymous_variant 0.14
embC 4241754 p.Ala631Val missense_variant 0.24
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242725 p.Gln955Lys missense_variant 0.12
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243983 c.751C>A synonymous_variant 0.13
embA 4244097 p.Tyr289Asn missense_variant 0.13
embA 4244879 c.1647C>A synonymous_variant 0.15
embA 4244900 c.1668G>C synonymous_variant 0.2
embB 4246049 c.-465G>A upstream_gene_variant 0.15
embB 4246722 p.Pro70Gln missense_variant 0.2
embB 4248392 c.1880delC frameshift_variant 0.14
embB 4249650 p.Ala1046Val missense_variant 0.18
embB 4249659 p.Met1049Lys missense_variant 0.2
embB 4249668 p.Tyr1052Cys missense_variant 0.2
aftB 4267821 p.Leu339Ser missense_variant 0.15
aftB 4268335 p.Ser168Gly missense_variant 0.13
aftB 4268366 p.Cys157Trp missense_variant 0.12
aftB 4268384 c.453G>A synonymous_variant 0.13
aftB 4269108 c.-272C>G upstream_gene_variant 0.1
ethA 4327578 c.-105C>G upstream_gene_variant 0.11
whiB6 4338244 p.Gly93Val missense_variant 0.12
whiB6 4338443 p.Tyr27His missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408119 c.84A>G synonymous_variant 0.15
gid 4408228 c.-26G>A upstream_gene_variant 0.14
gid 4408397 c.-195A>G upstream_gene_variant 0.14