TB-Profiler result

Run: ERR2228817
Summary

Run ID: ERR2228817

Sample name:

Date: 31-03-2023 16:21:53

Number of reads: 371783

Percentage reads mapped: 99.38

Strain: lineage4

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
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 5924 p.Ala229Ser missense_variant 0.38
gyrB 5996 p.Tyr253Asn missense_variant 0.75
gyrB 6100 c.861G>T synonymous_variant 0.67
gyrA 7353 p.Val18Ile missense_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7444 p.Leu48Arg missense_variant 0.5
gyrA 7539 p.Thr80Pro missense_variant 0.23
gyrA 7666 p.Asp122Ala missense_variant 0.42
gyrA 7704 p.Thr135Pro missense_variant 0.22
gyrA 8100 p.Thr267Pro missense_variant 0.2
gyrA 8992 p.His564Arg missense_variant 0.27
fgd1 491181 c.399T>G synonymous_variant 0.43
fgd1 491676 c.894T>G synonymous_variant 0.4
rpoB 759828 p.Lys8* stop_gained 0.29
rpoB 760804 p.Val333Glu missense_variant 0.33
rpoB 760822 p.Leu339Gln missense_variant 0.33
rpoB 761521 p.Tyr572Cys missense_variant 0.15
rpoB 762625 p.Val940Gly missense_variant 0.25
rpoB 763113 p.Gly1103Cys missense_variant 0.25
rpoC 763411 c.42T>C synonymous_variant 0.29
rpoC 764072 p.Ile235Leu missense_variant 0.25
rpoC 764695 c.1326T>C synonymous_variant 0.4
rpoC 765465 p.Asp699Ala missense_variant 0.18
rpoC 765603 p.Ile745Asn missense_variant 0.29
rpoC 766038 p.Asp890Ala missense_variant 0.29
rpoC 766823 p.Lys1152* stop_gained 0.33
rpoC 766871 p.Ile1168Val missense_variant 0.4
rpoC 767100 p.Lys1244Met missense_variant 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775643 c.2838A>C synonymous_variant 0.29
mmpL5 777041 c.1440G>T synonymous_variant 0.22
mmpL5 777219 p.Leu421Gln missense_variant 0.25
mmpL5 777502 p.Thr327Pro missense_variant 0.29
mmpL5 777691 p.Asn264Tyr missense_variant 0.29
mmpR5 779150 p.Glu54Val missense_variant 0.33
mmpS5 779678 c.-773T>G upstream_gene_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800822 p.Gly5Val missense_variant 0.22
rplC 801035 p.Asn76Thr missense_variant 0.33
fbiC 1303525 p.Ser199Ala missense_variant 0.33
fbiC 1303747 p.Thr273Ala missense_variant 1.0
Rv1258c 1406135 p.Glu402Asp missense_variant 0.4
Rv1258c 1407092 c.249T>G synonymous_variant 0.2
Rv1258c 1407144 p.Val66Gly missense_variant 0.22
Rv1258c 1407236 p.Leu35Phe missense_variant 0.25
embR 1416215 p.Phe378Tyr missense_variant 0.5
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471927 n.82T>A non_coding_transcript_exon_variant 0.33
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474456 n.799A>T non_coding_transcript_exon_variant 1.0
rrl 1476183 n.2526A>T non_coding_transcript_exon_variant 1.0
rrl 1476219 n.2562T>C non_coding_transcript_exon_variant 0.67
rpsA 1833541 c.-1T>A upstream_gene_variant 0.33
rpsA 1833543 c.2T>A start_lost 0.29
rpsA 1834836 p.Met432Lys missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918058 p.Val40Gly missense_variant 0.25
ndh 2102150 p.Asp298Val missense_variant 0.33
ndh 2102737 p.Glu102Asp missense_variant 0.33
katG 2154262 p.Leu617Arg missense_variant 0.38
katG 2154580 p.Asp511Ala missense_variant 0.29
katG 2154586 p.Asp509Ala missense_variant 0.22
katG 2155114 p.Leu333His missense_variant 0.33
katG 2155441 p.Gln224Leu missense_variant 0.2
katG 2155585 p.Met176Lys missense_variant 0.25
katG 2155756 p.Arg119His missense_variant 0.25
katG 2155850 p.Gln88Lys missense_variant 0.4
PPE35 2168088 p.Pro842Arg missense_variant 1.0
PPE35 2168600 c.2013G>T synonymous_variant 0.29
PPE35 2168728 p.Gly629Arg missense_variant 1.0
PPE35 2168732 c.1881T>A synonymous_variant 0.29
PPE35 2169269 c.1344A>G synonymous_variant 0.3
PPE35 2169272 c.1341C>G synonymous_variant 0.3
PPE35 2169278 c.1335T>C synonymous_variant 0.2
PPE35 2169281 c.1332T>G synonymous_variant 0.2
PPE35 2169287 c.1326T>C synonymous_variant 0.2
PPE35 2169293 c.1320T>C synonymous_variant 0.2
PPE35 2169308 c.1305C>T synonymous_variant 0.17
PPE35 2169510 p.Asn368Thr missense_variant 0.5
Rv1979c 2222687 p.Lys160* stop_gained 0.33
Rv1979c 2222705 p.Phe154Ile missense_variant 0.29
Rv1979c 2222733 p.Phe144Leu missense_variant 0.33
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518722 p.Glu203Ala missense_variant 0.22
kasA 2519167 c.1053T>G synonymous_variant 0.18
folC 2747138 p.Val154Gly missense_variant 0.4
folC 2747457 p.Thr48Pro missense_variant 0.3
folC 2747673 c.-75T>A upstream_gene_variant 0.67
folC 2747794 c.-196A>C upstream_gene_variant 0.25
pepQ 2859842 p.Ile193Phe missense_variant 0.29
pepQ 2860249 p.Asp57Ala missense_variant 0.3
ribD 2987010 p.Thr58Ala missense_variant 0.22
Rv2752c 3066319 c.-128T>G upstream_gene_variant 0.29
thyX 3067414 p.Ala178Ser missense_variant 0.22
thyX 3067910 c.36C>A synonymous_variant 0.67
thyX 3068070 c.-125T>A upstream_gene_variant 0.4
thyX 3068096 c.-151A>T upstream_gene_variant 0.33
thyX 3068130 c.-185A>T upstream_gene_variant 0.33
thyA 3074220 c.252A>T synonymous_variant 0.5
ald 3087183 p.Thr122Pro missense_variant 0.4
fbiD 3339066 c.-52C>A upstream_gene_variant 0.2
fbiD 3339417 p.Glu100Asp missense_variant 0.33
fbiD 3339634 p.Ser173Ala missense_variant 0.25
fprA 3473906 c.-101A>T upstream_gene_variant 0.3
Rv3236c 3612135 p.Thr328Ala missense_variant 0.33
Rv3236c 3613046 p.Val24Gly missense_variant 0.43
Rv3236c 3613085 p.Leu11Arg missense_variant 0.67
Rv3236c 3613095 p.Leu8Val missense_variant 0.67
fbiA 3640763 p.Asp74Ala missense_variant 0.4
fbiA 3641001 p.His153Gln missense_variant 0.25
alr 3840908 p.Gln171His missense_variant 0.33
rpoA 3878066 p.Pro148Thr missense_variant 0.4
ddn 3986915 c.72T>A synonymous_variant 0.33
clpC1 4039661 c.1044T>G synonymous_variant 0.43
clpC1 4040209 p.Ser166Ala missense_variant 0.25
clpC1 4040357 c.348T>G synonymous_variant 0.22
clpC1 4040409 p.Gly99Val missense_variant 0.14
embC 4239868 c.6T>G synonymous_variant 0.29
embC 4240694 p.Ile278Phe missense_variant 0.33
embC 4241043 p.Asn394Thr missense_variant 0.5
embC 4241450 p.Ser530Ala missense_variant 0.29
embC 4241705 p.Ser615Ala missense_variant 0.67
embC 4241726 p.Phe622Val missense_variant 0.75
embC 4242062 p.Trp734Arg missense_variant 0.22
embC 4242204 p.Leu781Gln missense_variant 0.33
embA 4242565 c.-668C>A upstream_gene_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243051 c.-182G>A upstream_gene_variant 0.17
embA 4243193 c.-40T>C upstream_gene_variant 0.25
embA 4244508 p.Leu426Val missense_variant 0.5
embA 4245177 p.Met649Leu missense_variant 0.22
embA 4246210 p.Phe993Tyr missense_variant 0.5
embB 4246544 p.Thr11Pro missense_variant 0.25
embB 4247004 p.Leu164Arg missense_variant 0.43
embB 4247028 p.Leu172Arg missense_variant 0.43
embB 4247156 p.Thr215Pro missense_variant 0.5
embB 4247445 p.Asp311Ala missense_variant 0.18
embB 4247470 c.957T>C synonymous_variant 0.17
embB 4247472 p.Phe320Tyr missense_variant 0.14
embB 4247538 p.His342Leu missense_variant 0.14
embB 4247817 p.Val435Ala missense_variant 0.22
embB 4247862 p.Ile450Ser missense_variant 0.22
embB 4248431 p.Trp640Gly missense_variant 0.27
embB 4249298 p.Trp929Gly missense_variant 0.25
embB 4249443 p.Tyr977Phe missense_variant 0.4
aftB 4267161 p.Val559Gly missense_variant 0.22
aftB 4267206 p.Val544Gly missense_variant 0.27
aftB 4267467 p.Tyr457Phe missense_variant 0.25
ubiA 4269448 p.Val129Gly missense_variant 0.4
ubiA 4269754 p.Val27Gly missense_variant 0.5
ubiA 4269833 c.1A>T initiator_codon_variant 0.5
ethA 4326581 p.Asn298Ile missense_variant 0.22
ethA 4327194 p.Ile94Phe missense_variant 0.22
ethR 4327288 c.-261T>A upstream_gene_variant 0.29
ethA 4328234 c.-761T>A upstream_gene_variant 0.23
whiB6 4338369 c.153C>A synonymous_variant 0.25
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407652 p.Val184Gly missense_variant 0.29