TB-Profiler result

Run: SRR12199429
Summary

Run ID: SRR12199429

Sample name:

Date: 03-04-2023 06:39:21

Number of reads: 774760

Percentage reads mapped: 65.3

Strain: lineage1.1.1

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
lineage1.1.1 Indo-Oceanic EAI4;EAI5 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 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490751 c.-32T>G upstream_gene_variant 0.27
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575700 p.Glu118Gly missense_variant 0.11
mshA 576123 p.Leu259Pro missense_variant 0.14
rpoB 760970 c.1164G>C synonymous_variant 0.11
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 765774 p.Ile802Asn missense_variant 0.25
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
fbiC 1303497 c.567G>T synonymous_variant 1.0
fbiC 1304083 p.Gly385Ser missense_variant 0.12
Rv1258c 1406406 p.Pro312Gln missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
fabG1 1673806 p.Ala123Thr missense_variant 0.12
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.24
PPE35 2170053 p.Thr187Ser missense_variant 0.22
PPE35 2170066 p.Ala183Thr missense_variant 0.2
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289842 c.-601G>T upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518879 c.765A>G synonymous_variant 0.12
kasA 2518882 c.768C>A synonymous_variant 0.12
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746562 p.Pro346His missense_variant 0.12
ribD 2987451 c.614_616delGTG disruptive_inframe_deletion 0.33
ribD 2987458 c.620_621insCAC disruptive_inframe_insertion 0.29
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074357 p.Ser39Ala missense_variant 1.0
thyA 3074378 p.Gln32Lys missense_variant 0.11
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339273 c.156T>G synonymous_variant 0.33
fbiD 3339477 c.360A>G synonymous_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
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 1.0
fbiB 3641665 p.Asp44Ala missense_variant 0.11
fbiB 3641693 c.159G>A synonymous_variant 0.13
alr 3841546 c.-126C>A upstream_gene_variant 0.19
rpoA 3877571 p.Pro313Ser missense_variant 1.0
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4040144 c.561G>C synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4242635 p.Ala925Thr missense_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243350 p.Thr40Pro missense_variant 0.22
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245209 c.1977G>A synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embA 4246272 p.Thr1014Ala missense_variant 1.0
embA 4246362 p.Thr1044Ala missense_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu missense_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 4407873 c.330G>T synonymous_variant 1.0