TB-Profiler result

Run: SRR18213958
Summary

Run ID: SRR18213958

Sample name:

Date: 03-04-2023 19:36:25

Number of reads: 2441352

Percentage reads mapped: 99.43

Strain: lineage4.4

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
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 5509 c.270C>T synonymous_variant 1.0
gyrB 5779 p.Phe180Leu missense_variant 0.17
gyrB 5821 c.582G>T synonymous_variant 0.14
gyrB 5848 c.609G>T synonymous_variant 0.14
gyrB 5915 p.Val226Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8829 c.1528T>C synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490777 c.-6G>T upstream_gene_variant 0.12
fgd1 491337 c.555C>G synonymous_variant 1.0
ccsA 620361 p.Tyr157* stop_gained 0.13
ccsA 620376 c.486G>A synonymous_variant 0.15
rpoB 760604 c.798G>A synonymous_variant 0.14
rpoB 760633 p.Arg276Leu missense_variant 0.11
rpoB 761157 p.Ala451Ser missense_variant 0.17
rpoB 762952 p.Gln1049Arg missense_variant 0.13
rpoC 763666 c.297G>A synonymous_variant 0.25
rpoC 764550 p.Pro394Leu missense_variant 0.2
rpoC 764890 c.1521G>A synonymous_variant 0.12
rpoC 765546 p.Arg726His missense_variant 0.13
rpoC 767145 p.Pro1259Gln missense_variant 0.12
mmpL5 775633 p.Gln950Lys missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776177 p.Leu768Phe missense_variant 0.13
mmpL5 777795 p.Ser229Trp missense_variant 0.11
mmpS5 778491 c.414delT frameshift_variant 0.2
mmpS5 778642 p.Trp88Cys missense_variant 0.29
mmpS5 778753 p.Phe51Leu missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800902 p.Gly32Trp missense_variant 0.12
fbiC 1302875 c.-56C>A upstream_gene_variant 0.15
fbiC 1302880 c.-51C>A upstream_gene_variant 0.14
fbiC 1302956 p.Ser9Tyr missense_variant 0.18
fbiC 1303497 c.567G>T synonymous_variant 0.15
Rv1258c 1407228 p.Glu38Ala missense_variant 1.0
Rv1258c 1407305 c.36C>A synonymous_variant 0.14
embR 1416605 p.Arg248Leu missense_variant 0.12
atpE 1460931 c.-113delT upstream_gene_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1473600 n.-57_-56delCG upstream_gene_variant 0.18
inhA 1674189 c.-13C>A upstream_gene_variant 0.12
rpsA 1833799 c.258C>A synonymous_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103151 c.-109G>T upstream_gene_variant 0.13
katG 2154587 p.Asp509Tyr missense_variant 0.12
katG 2155936 p.Gly59Asp missense_variant 0.12
PPE35 2167879 p.Ser912Gly missense_variant 0.17
PPE35 2168073 p.Pro847Gln missense_variant 0.2
PPE35 2170220 c.393C>A synonymous_variant 0.12
Rv1979c 2221857 p.Cys436* stop_gained 0.13
Rv1979c 2222224 p.Gly314Val missense_variant 0.18
Rv1979c 2223037 p.Ala43Val missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289911 c.-670G>A upstream_gene_variant 0.13
kasA 2518243 c.129C>A synonymous_variant 0.18
kasA 2518469 p.Ala119Pro missense_variant 0.11
eis 2715432 c.-100C>T upstream_gene_variant 0.12
eis 2715436 c.-104G>A upstream_gene_variant 0.12
eis 2715440 c.-108A>C upstream_gene_variant 0.12
eis 2715445 c.-113C>T upstream_gene_variant 0.12
eis 2715447 c.-115T>A upstream_gene_variant 0.12
eis 2715450 c.-118T>C upstream_gene_variant 0.12
eis 2715451 c.-119C>A upstream_gene_variant 0.11
eis 2715454 c.-122T>G upstream_gene_variant 0.11
eis 2715458 c.-126T>A upstream_gene_variant 0.11
eis 2715460 c.-128A>G upstream_gene_variant 0.11
eis 2715469 c.-137T>C upstream_gene_variant 0.12
eis 2715473 c.-141A>G upstream_gene_variant 0.12
ahpC 2726556 p.Ala122Thr missense_variant 0.12
folC 2746185 p.Val472Phe missense_variant 0.14
folC 2746319 p.Pro427Arg missense_variant 0.13
folC 2746555 c.1044G>T synonymous_variant 0.2
folC 2747153 p.Met149Thr missense_variant 0.17
pepQ 2859519 c.900G>T synonymous_variant 0.14
pepQ 2859665 p.Leu252Met missense_variant 0.14
pepQ 2860052 c.367C>A synonymous_variant 0.14
ribD 2986733 c.-106C>T upstream_gene_variant 0.12
ribD 2987168 c.330C>T synonymous_variant 0.4
ribD 2987378 c.540C>G synonymous_variant 0.1
ribD 2987583 p.Gly249Ser missense_variant 0.13
Rv2752c 3065265 c.927C>T synonymous_variant 0.4
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
Rv2752c 3066127 p.Gly22Val missense_variant 0.17
thyX 3068073 c.-128C>A upstream_gene_variant 0.12
thyA 3074483 c.-12C>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087399 p.Val194Phe missense_variant 0.13
fbiD 3339126 c.9C>A synonymous_variant 0.18
fbiD 3339200 p.Pro28Gln missense_variant 0.12
Rv3083 3448759 p.Ala86Thr missense_variant 0.18
Rv3083 3449110 p.Ser203Gly missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611997 p.Gly374Cys missense_variant 0.12
Rv3236c 3613224 c.-108C>G upstream_gene_variant 0.1
fbiA 3640941 p.Cys133* stop_gained 0.13
fbiA 3641179 p.Pro213Thr missense_variant 0.18
fbiB 3642189 p.Gly219Arg missense_variant 0.38
fbiB 3642621 p.Ala363Thr missense_variant 0.12
rpoA 3877648 p.Arg287Leu missense_variant 0.14
rpoA 3878099 p.Glu137Lys missense_variant 0.17
clpC1 4039250 c.1455C>T synonymous_variant 0.14
clpC1 4040173 p.Leu178Ile missense_variant 0.18
clpC1 4040545 p.Ile54Val missense_variant 0.14
embC 4241111 p.Val417Leu missense_variant 0.13
embC 4241197 c.1335G>C synonymous_variant 0.18
embC 4241361 p.Asn500Ser missense_variant 0.1
embC 4241752 p.Leu630Phe missense_variant 0.17
embC 4241889 p.Ala676Val missense_variant 0.17
embC 4242105 p.Thr748Asn missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243910 c.678G>A synonymous_variant 0.22
embA 4244635 c.1405delG frameshift_variant 0.14
embB 4245917 c.-597G>A upstream_gene_variant 0.12
embA 4246008 p.Arg926Trp missense_variant 0.17
embB 4246508 c.-6G>A upstream_gene_variant 1.0
embB 4249465 c.2952G>T synonymous_variant 0.11
aftB 4267536 p.Arg434Gln missense_variant 0.2
aftB 4268277 p.Pro187Leu missense_variant 0.14
aftB 4268513 c.324C>A synonymous_variant 0.12
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
ubiA 4269827 p.Glu3* stop_gained 0.18
ubiA 4269879 c.-46C>G upstream_gene_variant 0.17
ethA 4327590 c.-117G>A upstream_gene_variant 0.13
ethA 4327671 c.-198C>T upstream_gene_variant 0.15
ethA 4328115 c.-642G>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408185 c.18C>T synonymous_variant 0.22