TB-Profiler result

Run: ERR245817
Summary

Run ID: ERR245817

Sample name:

Date: 31-03-2023 18:22:48

Number of reads: 1693985

Percentage reads mapped: 98.96

Strain: lineage1.1.3.2

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
lineage1 Indo-Oceanic EAI RD239 1.0
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.99
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.2 Indo-Oceanic NA RD239 0.99
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 6112 p.Met291Ile missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8188 p.Leu296Pro missense_variant 0.96
gyrA 8445 p.Arg382Gly missense_variant 0.22
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9174 c.1873C>T synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 0.99
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.24
rpoB 759620 c.-187A>C upstream_gene_variant 0.21
rpoB 762249 p.Leu815Val missense_variant 0.19
rpoC 762836 c.-534C>G upstream_gene_variant 0.36
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764725 p.Phe452Leu missense_variant 0.4
rpoC 764905 p.Phe512Leu missense_variant 0.13
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
rpoC 767305 p.Tyr1312* stop_gained 0.25
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777399 p.Thr361Arg missense_variant 0.64
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781900 p.Arg114Pro missense_variant 0.2
rplC 801166 p.Gly120Ser missense_variant 1.0
fbiC 1303901 p.Val324Gly missense_variant 0.4
Rv1258c 1407522 c.-182C>G upstream_gene_variant 0.4
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417136 p.Ser71Ile missense_variant 0.4
embR 1417233 c.115C>T synonymous_variant 0.28
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473360 n.1515T>G non_coding_transcript_exon_variant 0.28
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.19
rrl 1475363 n.1706C>A non_coding_transcript_exon_variant 0.16
fabG1 1673449 p.Thr4Pro missense_variant 0.18
inhA 1674883 p.Ile228Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.23
katG 2154615 c.1497G>C synonymous_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 0.98
katG 2154758 p.Glu452Lys missense_variant 0.19
PPE35 2167926 p.Leu896Ser missense_variant 0.99
PPE35 2167983 p.Gly877Asp missense_variant 0.98
PPE35 2169866 c.747G>C synonymous_variant 0.44
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518891 c.777C>A synonymous_variant 0.22
eis 2714366 p.Val323Leu missense_variant 0.31
ahpC 2725954 c.-239C>T upstream_gene_variant 0.55
ahpC 2726051 c.-142G>A upstream_gene_variant 0.98
ahpC 2726756 c.564C>G synonymous_variant 0.24
folC 2746186 c.1413G>C synonymous_variant 0.4
pepQ 2859381 c.1038C>G synonymous_variant 0.25
pepQ 2859680 p.Leu247Val missense_variant 0.33
ribD 2987392 p.Arg185Pro missense_variant 0.15
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3064741 p.Gly484Ala missense_variant 0.42
thyX 3067965 c.-20C>G upstream_gene_variant 0.38
thyA 3073800 c.672G>C synonymous_variant 0.25
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448929 p.Tyr142* stop_gained 0.25
Rv3083 3449058 p.Ser185Arg missense_variant 0.64
Rv3083 3449673 p.Tyr390* stop_gained 0.34
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474079 p.Ala25Pro missense_variant 0.25
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475244 p.Arg413Pro missense_variant 0.25
Rv3236c 3612425 p.Ala231Gly missense_variant 0.5
Rv3236c 3612960 p.Ala53Pro missense_variant 0.33
fbiB 3641687 p.Lys51Asn missense_variant 0.12
fbiB 3641955 p.Gly141Arg missense_variant 0.4
fbiB 3642033 p.Ala167Pro missense_variant 0.27
fbiB 3642173 c.639G>A synonymous_variant 1.0
alr 3841472 c.-52C>G upstream_gene_variant 0.35
rpoA 3877766 p.Ala248Pro missense_variant 0.35
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
rpoA 3878692 c.-185C>G upstream_gene_variant 0.22
clpC1 4038857 c.1848C>A synonymous_variant 0.17
clpC1 4039363 p.Ala448Pro missense_variant 0.17
clpC1 4039932 p.Gly258Val missense_variant 0.29
clpC1 4040517 p.Val63Ala missense_variant 1.0
panD 4044406 c.-125C>G upstream_gene_variant 0.27
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 0.67
embC 4241128 c.1266G>C synonymous_variant 0.2
embC 4241429 p.Phe523Val missense_variant 0.43
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.5
embC 4242827 p.Leu989Val missense_variant 0.33
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244375 c.1143C>G synonymous_variant 0.33
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.47
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327672 c.-199G>A upstream_gene_variant 0.38
ethR 4328138 p.Ala197Gly missense_variant 0.26
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407780 c.423G>A synonymous_variant 0.95
gid 4407873 c.330G>T synonymous_variant 0.96
gid 4408273 c.-71C>G upstream_gene_variant 0.21