TB-Profiler result

Run: ERR245822
Summary

Run ID: ERR245822

Sample name:

Date: 31-03-2023 18:22:59

Number of reads: 2464009

Percentage reads mapped: 98.93

Strain: lineage1.1.3.2

Drug-resistance: Other

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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 0.99
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 1.0
lineage1.1.3 Indo-Oceanic EAI6 RD239 0.99
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
ethA 4327054 p.Tyr140* stop_gained 0.21 ethionamide
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 0.99
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7493 c.192C>T synonymous_variant 0.21
gyrA 7504 p.Arg68Pro missense_variant 0.42
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7655 c.354G>C synonymous_variant 0.23
gyrA 8188 p.Leu296Pro missense_variant 1.0
gyrA 8445 p.Arg382Gly missense_variant 0.35
gyrA 8452 p.Ala384Val missense_variant 0.98
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
ccsA 620407 p.Pro173Ala missense_variant 0.24
ccsA 620748 c.858T>G synonymous_variant 0.18
rpoB 759620 c.-187A>C upstream_gene_variant 0.29
rpoB 759831 p.Thr9Pro missense_variant 0.27
rpoB 761867 c.2061C>G synonymous_variant 0.33
rpoC 762836 c.-534C>G upstream_gene_variant 0.21
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 765171 p.Pro601Leu missense_variant 1.0
rpoC 765230 p.Ala621Thr missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 1.0
fbiC 1303669 p.Asp247Tyr missense_variant 0.25
Rv1258c 1407185 p.Met52Ile missense_variant 0.25
embR 1416445 p.Tyr301* stop_gained 0.27
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417136 p.Ser71Ile missense_variant 0.5
atpE 1461019 c.-26C>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473343 n.1498G>T non_coding_transcript_exon_variant 0.19
rrl 1474380 n.723G>T non_coding_transcript_exon_variant 0.26
rrl 1476408 n.2751G>C non_coding_transcript_exon_variant 0.2
fabG1 1673449 p.Thr4Pro missense_variant 0.24
fabG1 1673552 p.Asp38Ala missense_variant 0.33
inhA 1674883 p.Ile228Val missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918069 p.Thr44Pro missense_variant 0.5
tlyA 1918377 c.438T>G synonymous_variant 0.2
ndh 2102891 p.Phe51Ser missense_variant 0.23
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 0.99
PPE35 2169866 c.747G>C synonymous_variant 0.49
PPE35 2170156 p.Ala153Pro missense_variant 0.33
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
eis 2714297 p.Ala346Pro missense_variant 0.27
eis 2714366 p.Val323Leu missense_variant 0.22
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726550 p.Gln120Lys missense_variant 0.17
folC 2746186 c.1413G>C synonymous_variant 0.38
pepQ 2859381 c.1038C>G synonymous_variant 0.38
pepQ 2859680 p.Leu247Val missense_variant 0.4
Rv2752c 3064552 p.Arg547Pro missense_variant 0.23
Rv2752c 3064632 c.1560C>T synonymous_variant 0.97
Rv2752c 3064836 p.Leu452Phe missense_variant 0.4
thyA 3073817 p.Gln219Glu missense_variant 0.62
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087811 p.Ala331Gly missense_variant 0.25
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449058 p.Ser185Arg missense_variant 0.38
Rv3083 3449673 p.Tyr390* stop_gained 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475159 p.Asn385Asp missense_variant 0.97
fprA 3475305 c.1299C>G synonymous_variant 0.25
Rv3236c 3611982 p.Ala379Pro missense_variant 0.4
fbiA 3641271 p.Tyr243* stop_gained 0.19
fbiB 3641955 p.Gly141Arg missense_variant 0.33
fbiB 3642173 c.639G>A synonymous_variant 1.0
alr 3841504 c.-84C>G upstream_gene_variant 0.18
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
clpC1 4039363 p.Ala448Pro missense_variant 0.3
clpC1 4039932 p.Gly258Val missense_variant 0.31
clpC1 4040234 c.471C>G synonymous_variant 0.33
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240431 p.Gly190Ala missense_variant 0.44
embC 4240646 p.Phe262Val missense_variant 0.33
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241056 c.1194C>G synonymous_variant 0.3
embC 4241128 c.1266G>C synonymous_variant 0.44
embC 4241429 p.Phe523Val missense_variant 0.56
embC 4241456 p.Ala532Pro missense_variant 0.42
embA 4242442 c.-791G>A upstream_gene_variant 0.29
embC 4242587 p.Gly909Arg missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242822 p.Val987Gly missense_variant 0.32
embC 4242827 p.Leu989Val missense_variant 0.2
embA 4243848 p.Val206Met missense_variant 1.0
embA 4243977 p.Ala249Pro missense_variant 0.4
embA 4244375 c.1143C>G synonymous_variant 0.25
embB 4245713 c.-801G>C upstream_gene_variant 0.17
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249618 c.3105C>G synonymous_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269529 p.Ala102Gly missense_variant 0.29
aftB 4269606 c.-770T>C upstream_gene_variant 0.97
ethA 4327672 c.-199G>A upstream_gene_variant 0.36
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 1.0
gid 4407873 c.330G>T synonymous_variant 1.0