TB-Profiler result

Run: SRR11972243
Summary

Run ID: SRR11972243

Sample name:

Date: 03-04-2023 05:33:19

Number of reads: 607137

Percentage reads mapped: 99.14

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 1.0
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 5619 p.Val127Glu missense_variant 0.12
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 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 490963 p.Val61Ile missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575470 c.123A>G synonymous_variant 0.12
mshA 575788 c.441C>T synonymous_variant 0.12
ccsA 619695 c.-196G>A upstream_gene_variant 1.0
rpoB 759709 c.-98C>T upstream_gene_variant 0.13
rpoB 762327 p.Val841Leu missense_variant 0.33
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoB 763063 p.Lys1086Arg missense_variant 0.22
rpoB 763183 p.Cys1126Tyr missense_variant 0.17
rpoC 763339 c.-31T>C upstream_gene_variant 0.18
rpoC 763661 p.Ala98Ser missense_variant 0.13
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 765570 p.Ala734Val missense_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776778 p.Arg568His missense_variant 0.12
mmpL5 777541 p.Gly314Ser missense_variant 0.17
mmpL5 778314 p.Val56Ala missense_variant 0.12
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801166 p.Gly120Ser missense_variant 1.0
fbiC 1304429 p.Arg500Gln missense_variant 0.12
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1475396 n.1739C>T non_coding_transcript_exon_variant 0.12
rpsA 1834337 p.Asp266Asn missense_variant 0.2
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154225 c.1887T>C synonymous_variant 0.15
katG 2154638 p.Ala492Thr missense_variant 0.25
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 2169902 p.Leu237Phe missense_variant 0.29
PPE35 2169910 p.Asn235Tyr missense_variant 0.26
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 2518452 p.Gly113Asp missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
pepQ 2859721 p.Met233Thr missense_variant 0.19
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087807 p.Arg330Trp missense_variant 0.12
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3449689 p.Thr396Ala missense_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474168 c.162G>T synonymous_variant 0.33
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3475102 p.Gly366Trp missense_variant 0.22
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475306 p.Gly434Ser missense_variant 0.33
Rv3236c 3612244 c.873T>A synonymous_variant 0.15
Rv3236c 3612797 p.Ala107Glu missense_variant 0.13
Rv3236c 3613210 c.-94A>T upstream_gene_variant 0.12
fbiB 3642173 c.639G>A synonymous_variant 1.0
alr 3841546 c.-126C>A upstream_gene_variant 0.13
rpoA 3877579 p.Asp310Val missense_variant 0.25
rpoA 3878687 c.-180A>C upstream_gene_variant 1.0
ddn 3987089 c.246G>A synonymous_variant 0.13
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240903 c.1041C>A synonymous_variant 0.14
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241502 p.Ser547* stop_gained 0.22
embC 4241609 p.Pro583Thr missense_variant 0.29
embC 4241792 p.Ser644Pro missense_variant 0.33
embC 4241924 p.Arg688Cys missense_variant 0.25
embC 4242087 p.Gln742Arg missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242666 p.Ala935Val missense_variant 0.25
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244746 p.Leu505His missense_variant 0.29
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4247903 p.Arg464Trp missense_variant 0.25
embB 4249074 p.Gln854Leu missense_variant 0.12
embB 4249095 p.Ala861Val missense_variant 0.2
aftB 4268363 p.Trp158Cys missense_variant 0.14
aftB 4268898 c.-62G>T upstream_gene_variant 0.18
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_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
gid 4407922 p.Leu94Pro missense_variant 0.29
gid 4408354 c.-152G>A upstream_gene_variant 1.0