TB-Profiler result

Run: SRR4033450
Summary

Run ID: SRR4033450

Sample name:

Date: 04-04-2023 06:06:26

Number of reads: 637798

Percentage reads mapped: 99.66

Strain: lineage4.3.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.2 Euro-American (LAM) LAM3 None 0.98
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 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
gyrB 5159 c.-81C>T upstream_gene_variant 0.29
gyrB 5512 c.273C>T synonymous_variant 0.33
gyrB 5520 p.Pro94Leu missense_variant 0.83
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7367 p.Gln22His missense_variant 0.5
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8463 p.Ala388Pro missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491144 p.Ala121Asp missense_variant 0.29
mshA 575737 p.Cys130* stop_gained 0.12
rpoB 761854 p.Ile683Asn missense_variant 0.4
rpoB 763090 c.3284_3285insT frameshift_variant 0.4
rpoB 763321 p.Ala1172Val missense_variant 0.22
rpoC 763898 p.Leu177Val missense_variant 0.22
rpoC 764995 c.1626C>G synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777182 c.1299C>A synonymous_variant 0.33
mmpL5 777869 c.612G>A synonymous_variant 0.14
mmpL5 777997 p.Ala162Thr missense_variant 0.22
mmpL5 778017 p.Gly155Val missense_variant 0.29
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781721 c.162C>T synonymous_variant 0.22
rplC 800644 c.-165G>A upstream_gene_variant 0.25
rplC 800651 c.-158G>A upstream_gene_variant 0.25
rplC 800704 c.-105T>C upstream_gene_variant 0.22
fbiC 1303000 p.Ser24Pro missense_variant 0.12
fbiC 1304185 p.Asp419Tyr missense_variant 0.15
fbiC 1304230 p.Pro434Ser missense_variant 0.14
fbiC 1304776 p.Asp616Tyr missense_variant 0.13
fbiC 1304791 p.Val621Ile missense_variant 0.13
fbiC 1305292 c.2365delG frameshift_variant 0.15
Rv1258c 1406689 p.Phe218Ile missense_variant 0.15
Rv1258c 1407486 c.-146A>G upstream_gene_variant 0.25
embR 1416603 p.Ala249Thr missense_variant 0.2
embR 1417051 c.297G>T synonymous_variant 0.13
embR 1417433 c.-86T>C upstream_gene_variant 0.22
embR 1417515 c.-168T>C upstream_gene_variant 0.13
rrs 1472337 n.492C>T non_coding_transcript_exon_variant 0.75
rpsA 1833683 c.142C>A synonymous_variant 0.25
rpsA 1834175 p.Arg212Gly missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1917980 p.Arg14Gln missense_variant 0.5
tlyA 1917996 c.57A>T synonymous_variant 0.4
tlyA 1918276 p.Val113Ile missense_variant 0.17
ndh 2101984 c.1059C>G synonymous_variant 0.14
ndh 2102135 p.Val303Ala missense_variant 0.22
ndh 2102551 c.492G>T synonymous_variant 0.18
ndh 2103021 p.Thr8Ala missense_variant 0.13
ndh 2103042 c.1A>T initiator_codon_variant 0.15
katG 2156494 c.-383A>T upstream_gene_variant 0.4
PPE35 2168671 p.Gly648Cys missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289238 c.4C>A synonymous_variant 0.15
pncA 2289261 c.-20C>T upstream_gene_variant 0.15
kasA 2518920 p.Gly269Asp missense_variant 0.15
kasA 2518926 p.Thr271Asn missense_variant 0.15
eis 2715404 c.-72G>A upstream_gene_variant 0.19
ahpC 2726199 p.Leu3Val missense_variant 0.18
folC 2746360 c.1239T>C synonymous_variant 0.13
folC 2747426 p.Gly58Asp missense_variant 0.15
pepQ 2860084 p.Gly112Asp missense_variant 0.12
pepQ 2860484 c.-66G>A upstream_gene_variant 0.17
pepQ 2860532 c.-114G>A upstream_gene_variant 0.14
Rv2752c 3065459 p.Val245Ile missense_variant 0.33
Rv2752c 3065475 c.717C>T synonymous_variant 0.33
Rv2752c 3066285 c.-94C>A upstream_gene_variant 0.2
thyX 3067284 p.Ala221Val missense_variant 0.15
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086868 p.Ala17Thr missense_variant 0.29
ald 3086922 p.Ile35Phe missense_variant 0.33
fbiD 3338993 c.-125C>T upstream_gene_variant 0.14
fbiD 3339036 c.-82A>G upstream_gene_variant 0.11
fbiD 3339512 p.Ala132Glu missense_variant 0.15
fbiD 3339525 c.408G>T synonymous_variant 0.15
fprA 3473959 c.-48A>T upstream_gene_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.86
Rv3236c 3612312 p.Leu269Met missense_variant 0.18
fbiA 3640800 p.Trp86Cys missense_variant 0.14
fbiB 3642080 c.546A>T synonymous_variant 0.25
fbiB 3642370 p.Ala279Val missense_variant 0.25
alr 3840602 c.819G>C synonymous_variant 0.11
alr 3840667 p.Arg252Trp missense_variant 0.2
alr 3841029 p.Ala131Val missense_variant 0.2
alr 3841069 p.Ile118Val missense_variant 0.18
alr 3841070 c.350delG frameshift_variant 0.18
rpoA 3877890 c.618C>T synonymous_variant 0.2
rpoA 3877900 c.607delA frameshift_variant 0.22
ddn 3986645 c.-199G>A upstream_gene_variant 0.15
ddn 3986968 p.Gln42Arg missense_variant 0.2
ddn 3986981 c.138C>T synonymous_variant 0.22
ddn 3986988 c.145C>T synonymous_variant 0.22
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040846 c.-142A>G upstream_gene_variant 0.11
embC 4239986 p.Val42Met missense_variant 0.18
embC 4240319 p.Gln153Glu missense_variant 0.14
embC 4240675 c.814_815dupGG frameshift_variant 0.2
embC 4240709 p.Trp283Arg missense_variant 0.2
embC 4241420 p.Glu520Lys missense_variant 0.12
embC 4241527 c.1665C>T synonymous_variant 0.12
embC 4241611 c.1749G>C synonymous_variant 0.2
embC 4242558 p.Gln899Leu missense_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243547 c.315G>T synonymous_variant 0.22
embA 4243827 p.Pro199Ser missense_variant 0.15
embA 4244841 p.Arg537Gly missense_variant 0.17
embA 4244942 p.Trp570Cys missense_variant 0.2
embA 4245696 p.Asn822Tyr missense_variant 0.12
embB 4245992 c.-522C>A upstream_gene_variant 0.18
embA 4246015 p.Pro928Gln missense_variant 0.18
embB 4249361 p.Ala950Pro missense_variant 0.13
aftB 4267251 p.Asp529Val missense_variant 0.2
aftB 4267282 p.Glu519Gln missense_variant 0.18
aftB 4267297 c.1540T>C synonymous_variant 0.18
aftB 4267583 c.1254C>T synonymous_variant 0.2
aftB 4267613 c.1224C>T synonymous_variant 0.4
aftB 4267646 c.1191C>T synonymous_variant 0.29
aftB 4267667 c.1170A>G synonymous_variant 0.25
ubiA 4269721 p.Ala38Val missense_variant 0.13
ubiA 4269773 p.Ile21Val missense_variant 0.22
aftB 4269801 c.-965A>G upstream_gene_variant 0.15
ethA 4326444 p.Leu344Met missense_variant 0.2
whiB6 4338550 c.-29A>G upstream_gene_variant 0.2
whiB6 4338579 c.-58C>G upstream_gene_variant 0.22
whiB6 4338593 c.-72C>A upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407958 p.Ala82Val missense_variant 0.25
gid 4408156 p.Leu16Arg missense_variant 1.0