TB-Profiler result

Run: SRR12199426
Summary

Run ID: SRR12199426

Sample name:

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

Number of reads: 410406

Percentage reads mapped: 97.09

Strain: lineage1.1.3.1

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
lineage1.1.3 Indo-Oceanic EAI6 RD239 1.0
lineage1.1.3.1 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
gyrB 6180 p.Gly314Asp missense_variant 0.15
gyrB 6198 p.Phe320Cys missense_variant 0.17
gyrB 6582 p.Thr448Met missense_variant 0.25
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8328 p.Ala343Thr missense_variant 0.13
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
gyrA 9352 p.Ser684Leu missense_variant 0.14
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575776 c.429C>T synonymous_variant 0.15
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763291 p.Arg1162His missense_variant 0.14
rpoC 763884 p.Ala172Val missense_variant 1.0
rpoC 763886 c.517C>A synonymous_variant 1.0
rpoC 764783 p.Ala472Thr missense_variant 0.17
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
mmpL5 776335 p.Val716Met missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801215 p.Gly136Ala missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918741 p.Pro268Thr missense_variant 0.2
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167814 c.2799C>T synonymous_variant 0.15
PPE35 2167865 c.2748G>C synonymous_variant 0.23
PPE35 2167868 c.2745A>C synonymous_variant 0.23
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169269 c.1344A>G synonymous_variant 0.31
PPE35 2169272 c.1341C>G synonymous_variant 0.29
PPE35 2169278 c.1335T>C synonymous_variant 0.41
PPE35 2169281 c.1332T>G synonymous_variant 0.29
PPE35 2169287 c.1326T>C synonymous_variant 0.21
PPE35 2169293 c.1320T>C synonymous_variant 0.11
PPE35 2170048 p.Leu189Val missense_variant 0.5
PPE35 2170053 p.Thr187Ser missense_variant 0.43
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518048 c.-67C>T upstream_gene_variant 0.13
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518325 p.His71Asn missense_variant 1.0
kasA 2518864 c.750G>C synonymous_variant 0.38
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746171 c.1428G>T synonymous_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
thyA 3074318 p.Phe52Leu missense_variant 0.29
ald 3086786 c.-34C>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
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
whiB7 3568580 p.Ala34Ser missense_variant 0.13
fbiB 3641966 c.432C>T synonymous_variant 0.33
alr 3841253 c.168C>T synonymous_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.24
clpC1 4040144 c.561G>C synonymous_variant 0.4
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 4243346 p.Gln38His missense_variant 0.22
embA 4243848 p.Val206Met missense_variant 1.0
embA 4243998 p.Ala256Thr missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246791 p.Pro93Leu missense_variant 1.0
embB 4247470 c.957T>C synonymous_variant 0.5
embB 4247472 p.Phe320Tyr missense_variant 0.5
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267175 c.1662C>T synonymous_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
ubiA 4269491 p.Ala115Thr missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
whiB6 4338207 c.315G>T synonymous_variant 0.18
whiB6 4338431 p.Leu31Val missense_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
whiB6 4338429 c.-218_92del frameshift_variant&start_lost 1.0