TB-Profiler result

Run: SRR21277753

Summary

Run ID: SRR21277753

Sample name:

Date: 04-04-2023 01:39:21

Number of reads: 8496775

Percentage reads mapped: 97.91

Strain: lineage4.4.2

Drug-resistance: Sensitive


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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
lineage4.4 Euro-American S;T None 1.0
lineage4.4.2 Euro-American T1;T2 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
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 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7618 p.Arg106Leu missense_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 0.99
mshA 575656 c.309G>A synonymous_variant 0.12
mshA 575835 p.Trp163* stop_gained 0.25
mshA 575906 p.Ala187Thr missense_variant 1.0
mshA 576443 p.Gly366Ser missense_variant 0.25
mshA 576462 p.Ala372Glu missense_variant 1.0
rpoB 761691 p.Ala629Ser missense_variant 0.23
rpoB 762780 p.Gly992Cys missense_variant 0.21
rpoC 763926 p.Ala186Asp missense_variant 0.29
rpoC 765288 p.Leu640Gln missense_variant 0.13
rpoC 765294 p.Pro642Gln missense_variant 0.15
rpoC 765303 p.Glu645Val missense_variant 0.1
rpoC 766048 c.2679C>A synonymous_variant 0.29
rpoC 766099 c.2730G>T synonymous_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 0.99
mmpL5 777308 c.1173C>T synonymous_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303098 c.168C>A synonymous_variant 0.25
fbiC 1303128 c.198C>T synonymous_variant 0.25
fbiC 1303132 p.Ala68Ser missense_variant 0.15
fbiC 1303905 c.975G>A synonymous_variant 0.11
fbiC 1305454 p.Arg842Ser missense_variant 0.13
Rv1258c 1406169 p.Gly391Val missense_variant 0.12
embR 1416959 p.Arg130Leu missense_variant 0.1
embR 1416961 c.387C>T synonymous_variant 0.15
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1674842 p.Gln214Leu missense_variant 0.13
rpsA 1833343 c.-199G>T upstream_gene_variant 0.13
tlyA 1917850 c.-90C>G upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918086 c.147C>T synonymous_variant 0.4
tlyA 1918541 p.Pro201Gln missense_variant 0.1
tlyA 1918610 p.Gly224Val missense_variant 0.12
ndh 2101696 c.1347C>A synonymous_variant 0.1
ndh 2102374 c.669G>T synonymous_variant 0.1
katG 2155767 c.345C>A synonymous_variant 0.25
katG 2155779 c.333C>A synonymous_variant 0.13
PPE35 2170424 c.189G>A synonymous_variant 0.4
PPE35 2170515 p.Gly33Glu missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519020 c.906G>A synonymous_variant 0.43
eis 2715012 c.321C>T synonymous_variant 0.11
eis 2715077 p.Ala86Ser missense_variant 0.12
eis 2715553 c.-221C>T upstream_gene_variant 0.1
folC 2746303 c.1296C>T synonymous_variant 0.22
folC 2746587 p.Arg338Trp missense_variant 0.13
folC 2746879 p.Lys240Asn missense_variant 0.1
folC 2747697 c.-99G>A upstream_gene_variant 0.1
pepQ 2859611 p.Leu270Met missense_variant 0.25
pepQ 2859624 c.795G>A synonymous_variant 0.14
pepQ 2859924 c.495G>T synonymous_variant 0.2
pepQ 2859979 p.Cys147Tyr missense_variant 0.1
pepQ 2860133 p.Gly96Cys missense_variant 0.16
ribD 2987295 p.Arg153Ser missense_variant 0.1
ribD 2987362 p.Glu175Val missense_variant 0.15
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
Rv2752c 3066291 c.-100G>T upstream_gene_variant 0.18
Rv2752c 3066304 c.-113C>A upstream_gene_variant 0.18
Rv2752c 3067187 c.-996C>T upstream_gene_variant 0.17
thyX 3067550 c.396G>A synonymous_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339052 c.-66G>T upstream_gene_variant 0.13
fbiD 3339055 c.-63C>T upstream_gene_variant 0.12
fbiD 3339349 p.Asp78Tyr missense_variant 0.12
fbiD 3339556 p.Gly147Ser missense_variant 0.4
Rv3083 3448727 p.Leu75Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568505 p.Arg59Gly missense_variant 1.0
Rv3236c 3612149 p.Gln323Leu missense_variant 0.12
Rv3236c 3612178 c.939C>A synonymous_variant 0.12
fbiB 3642395 c.861A>T synonymous_variant 0.11
fbiB 3642659 c.1125C>A synonymous_variant 0.12
alr 3841168 p.Gly85Cys missense_variant 0.29
clpC1 4039058 p.Phe549Leu missense_variant 1.0
clpC1 4039606 p.Glu367Lys missense_variant 0.1
clpC1 4040228 c.477G>T synonymous_variant 0.12
panD 4044473 c.-192G>T upstream_gene_variant 0.12
embC 4240587 p.Gly242Asp missense_variant 0.12
embC 4241247 p.Arg462Gln missense_variant 0.14
embC 4241249 p.Arg463Cys missense_variant 0.14
embC 4242163 c.2301G>A synonymous_variant 0.12
embC 4242184 c.2322C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243858 p.Leu209His missense_variant 0.12
embA 4243971 p.Gly247Arg missense_variant 0.18
embA 4243991 c.759T>G synonymous_variant 0.96
embA 4243996 p.Ala255Val missense_variant 0.11
embA 4244432 c.1200C>A synonymous_variant 0.18
embA 4244601 p.Ala457Ser missense_variant 0.25
embA 4244858 c.1626G>A synonymous_variant 0.17
embB 4245668 c.-846C>A upstream_gene_variant 0.12
embA 4245822 p.Pro864Ser missense_variant 0.11
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4246798 c.285C>T synonymous_variant 0.11
embB 4247146 c.633C>A synonymous_variant 1.0
embB 4247283 p.Arg257Leu missense_variant 0.11
embB 4247636 p.Pro375Thr missense_variant 0.2
embB 4248584 c.2071_2073delCGCinsAGA synonymous_variant 0.15
aftB 4267970 p.Phe289Leu missense_variant 0.12
aftB 4268278 p.Pro187Thr missense_variant 0.11
aftB 4268855 c.-19G>T upstream_gene_variant 0.18
aftB 4268869 c.-33C>A upstream_gene_variant 0.18
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ubiA 4269719 p.Ala39Ser missense_variant 0.11
aftB 4269732 c.-896C>A upstream_gene_variant 0.15
ethR 4326889 c.-660C>A upstream_gene_variant 0.14
ethR 4327603 p.Arg19Trp missense_variant 0.17
ethR 4328039 p.Arg164Leu missense_variant 0.11
ethA 4328049 c.-576C>A upstream_gene_variant 0.1
whiB6 4338343 p.Trp60* stop_gained 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0