TB-Profiler result

Run: ERR9901059
Summary

Run ID: ERR9901059

Sample name:

Date: 02-04-2023 13:32:04

Number of reads: 698291

Percentage reads mapped: 99.16

Strain: lineage1.1.3

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 1.0
lineage1.1.3 Indo-Oceanic EAI6 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 5436 p.Asn66Ser missense_variant 1.0
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 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.97
fgd1 491334 c.552C>T synonymous_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576221 c.877dupG frameshift_variant 0.2
mshA 576423 p.Ala359Asp missense_variant 0.11
mshA 576727 c.1380A>T synonymous_variant 0.17
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
rpoC 766045 p.Gln892His missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777291 p.Ala397Gly missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781458 c.-102C>T upstream_gene_variant 1.0
rplC 800702 c.-106delT upstream_gene_variant 0.11
fbiC 1304458 p.Thr510Ser missense_variant 0.12
fbiC 1304575 p.Asn549Asp missense_variant 0.14
Rv1258c 1407158 c.183C>A synonymous_variant 0.29
Rv1258c 1407180 p.Pro54Gln missense_variant 0.22
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834522 c.981C>T synonymous_variant 0.12
rpsA 1834563 p.Gly341Val missense_variant 0.11
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154911 p.Pro401Thr missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.21
PPE35 2170053 p.Thr187Ser missense_variant 0.21
PPE35 2170614 c.-2C>T upstream_gene_variant 1.0
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290222 c.-981C>A upstream_gene_variant 0.18
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519255 p.Asp381Tyr missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746361 p.Asp413Gly missense_variant 0.12
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065540 p.Val218Leu missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339419 p.Arg101His missense_variant 0.13
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449106 c.603C>G synonymous_variant 0.13
Rv3083 3449147 p.Ser215* stop_gained 0.14
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474130 c.124T>C synonymous_variant 0.11
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474811 p.Phe269Leu missense_variant 0.11
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475217 c.1213delC frameshift_variant 0.12
Rv3236c 3612803 p.Ala105Val missense_variant 0.12
fbiB 3642215 c.681G>T synonymous_variant 0.18
fbiB 3642264 p.Gly244Arg missense_variant 0.2
rpoA 3878688 c.-181C>A upstream_gene_variant 0.5
clpC1 4038195 p.Ala837Gly missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245511 p.Pro760Gln missense_variant 0.18
embB 4245575 c.-939C>A upstream_gene_variant 0.15
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246548 p.Pro12Gln missense_variant 0.12
embB 4246555 c.42G>C synonymous_variant 0.12
embB 4246556 p.Ala15Pro missense_variant 0.12
embB 4246918 c.405G>T synonymous_variant 0.14
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267945 p.Tyr298His missense_variant 0.14
aftB 4267948 p.Asp297Tyr missense_variant 0.14
aftB 4268523 p.Leu105Ser missense_variant 0.13
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327638 c.-165G>T upstream_gene_variant 0.12
whiB6 4338243 c.278delG frameshift_variant 1.0
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