TB-Profiler result

Run: SRR1187037
Summary

Run ID: SRR1187037

Sample name:

Date: 03-04-2023 05:21:47

Number of reads: 844344

Percentage reads mapped: 99.28

Strain: lineage4.1.2

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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.2 Euro-American T;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 5235 c.-5G>T upstream_gene_variant 0.14
gyrB 5249 p.Gln4Lys missense_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7667 p.Asp122Glu missense_variant 0.14
gyrA 7673 c.372G>A synonymous_variant 0.2
gyrA 8186 p.Lys295Asn missense_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491203 p.Gln141Lys missense_variant 0.17
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575436 p.Pro30Gln missense_variant 0.14
mshA 575606 p.Glu87* stop_gained 0.13
mshA 575821 c.474G>T synonymous_variant 0.17
mshA 576356 p.Ala337Ser missense_variant 0.17
ccsA 619762 c.-129C>A upstream_gene_variant 0.15
ccsA 620101 p.Pro71Thr missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760496 c.690G>T synonymous_variant 0.12
rpoB 760545 p.Gly247Trp missense_variant 0.15
rpoB 761296 p.Tyr497Cys missense_variant 0.2
rpoB 761673 p.Gly623Trp missense_variant 0.15
rpoB 761969 p.Glu721Asp missense_variant 0.12
rpoB 762772 p.Asn989Ser missense_variant 0.12
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765634 p.Lys755Asn missense_variant 0.17
mmpL5 775589 c.2892C>A synonymous_variant 0.15
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776902 p.Asn527Asp missense_variant 0.11
mmpL5 777746 c.735G>A synonymous_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781763 c.204C>A synonymous_variant 0.25
rplC 800884 p.Val26Met missense_variant 0.12
fbiC 1304862 p.Lys644Asn missense_variant 0.12
fbiC 1305088 p.Val720Ile missense_variant 0.11
Rv1258c 1406484 p.Pro286His missense_variant 0.13
Rv1258c 1406512 p.Gly277Trp missense_variant 0.12
Rv1258c 1406744 c.597G>T synonymous_variant 0.12
Rv1258c 1406776 p.Ala189Ser missense_variant 0.13
Rv1258c 1407370 c.-30G>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472632 n.787C>T non_coding_transcript_exon_variant 0.12
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.13
rrl 1473942 n.285G>T non_coding_transcript_exon_variant 0.15
rrl 1475257 n.1600C>A non_coding_transcript_exon_variant 0.22
inhA 1673571 c.-631C>T upstream_gene_variant 0.15
inhA 1674470 p.Gly90Val missense_variant 0.25
rpsA 1834538 p.Val333Leu missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102174 p.Ala290Asp missense_variant 0.12
katG 2155456 p.Pro219Gln missense_variant 0.22
katG 2156438 c.-327C>A upstream_gene_variant 0.12
PPE35 2169964 p.Leu217Val missense_variant 0.11
Rv1979c 2222401 p.Ala255Asp missense_variant 0.12
Rv1979c 2222473 p.Ala231Glu missense_variant 0.12
Rv1979c 2222775 c.390C>A synonymous_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290064 c.-823C>T upstream_gene_variant 0.17
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
kasA 2518161 p.Val16Gly missense_variant 0.2
kasA 2518237 p.Ser41Arg missense_variant 0.18
kasA 2519053 c.939G>T synonymous_variant 0.13
ahpC 2726705 c.513C>T synonymous_variant 0.12
folC 2746300 c.1299C>T synonymous_variant 0.18
folC 2747685 c.-87C>A upstream_gene_variant 0.25
pepQ 2860565 c.-147C>T upstream_gene_variant 0.17
ribD 2987127 p.Arg97Trp missense_variant 0.15
ribD 2987568 p.Leu244Ile missense_variant 0.12
Rv2752c 3065343 c.849T>C synonymous_variant 0.1
Rv2752c 3067035 c.-844C>A upstream_gene_variant 0.15
Rv2752c 3067131 c.-940G>T upstream_gene_variant 0.18
thyX 3067356 p.Ala197Val missense_variant 0.2
thyX 3067393 p.Val185Leu missense_variant 0.22
thyA 3074645 c.-174T>G upstream_gene_variant 0.22
thyA 3074656 c.-185G>T upstream_gene_variant 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087206 c.387G>A synonymous_variant 0.13
ald 3087497 p.Glu226Asp missense_variant 0.12
ald 3087862 p.Gly348Val missense_variant 0.12
Rv3083 3449566 p.Gly355Arg missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474862 p.Arg286Trp missense_variant 0.12
Rv3236c 3612749 p.Gly123Val missense_variant 0.14
fbiA 3641333 p.Gly264Val missense_variant 0.15
fbiB 3641895 p.Leu121Met missense_variant 0.15
rpoA 3878551 c.-44C>A upstream_gene_variant 0.22
rpoA 3878630 c.-123G>C upstream_gene_variant 0.15
clpC1 4039355 c.1350G>A synonymous_variant 0.14
clpC1 4039542 p.Arg388Leu missense_variant 0.14
clpC1 4040880 c.-176G>T upstream_gene_variant 0.12
embC 4239866 p.Ala2Ser missense_variant 0.15
embC 4240822 c.960C>A synonymous_variant 0.14
embC 4241682 p.Ala607Val missense_variant 0.25
embC 4241711 p.Arg617Trp missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embA 4243782 p.Gly184Trp missense_variant 0.18
embB 4246547 p.Pro12Thr missense_variant 0.13
embB 4246687 p.Trp58Cys missense_variant 0.12
embB 4246700 p.Gln63Lys missense_variant 0.12
embB 4246888 c.375C>T synonymous_variant 0.17
embB 4246939 c.426C>A synonymous_variant 0.17
embB 4246999 c.486C>T synonymous_variant 0.18
embB 4247347 c.834G>T synonymous_variant 0.12
embB 4249397 p.Ala962Thr missense_variant 0.14
aftB 4267299 p.Pro513Gln missense_variant 0.13
aftB 4267732 p.Arg369Ser missense_variant 0.13
aftB 4267787 c.1050G>C synonymous_variant 0.2
aftB 4268445 p.Ala131Asp missense_variant 0.15
ubiA 4269073 p.Pro254Arg missense_variant 0.17
ubiA 4269867 c.-34G>A upstream_gene_variant 0.15
ubiA 4269924 c.-91G>A upstream_gene_variant 0.15
ethA 4327728 c.-255C>T upstream_gene_variant 1.0
whiB6 4338239 p.Leu95Met missense_variant 0.12
whiB6 4338243 c.279C>A synonymous_variant 0.12
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408310 c.-108G>A upstream_gene_variant 0.12