TB-Profiler result

Run: SRR11972245
Summary

Run ID: SRR11972245

Sample name:

Date: 03-04-2023 05:33:21

Number of reads: 325883

Percentage reads mapped: 99.31

Strain: lineage1.1.2

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 0.98
lineage1.1.2 Indo-Oceanic EAI3;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
gyrB 6124 c.885C>T synonymous_variant 1.0
gyrA 7069 c.-233C>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8064 p.Gly255Arg missense_variant 0.17
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9047 c.1746C>T synonymous_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9443 c.2142G>A synonymous_variant 0.96
fgd1 491483 p.Ser234Tyr missense_variant 0.15
fgd1 491603 p.Ala274Val missense_variant 0.13
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575191 c.-156delA upstream_gene_variant 0.12
mshA 575227 c.-121C>G upstream_gene_variant 0.17
mshA 575284 c.-64C>G upstream_gene_variant 0.86
mshA 576000 p.Asp218Ala missense_variant 0.92
rpoB 760490 c.684C>T synonymous_variant 0.86
rpoB 760867 p.Gly354Asp missense_variant 0.33
rpoB 761961 p.Pro719Ser missense_variant 0.17
rpoB 762507 p.Leu901Ile missense_variant 0.2
rpoB 762619 p.Trp938* stop_gained 0.15
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 763986 p.Arg206His missense_variant 0.29
rpoC 765171 p.Pro601Leu missense_variant 1.0
rpoC 765360 p.Ala664Val missense_variant 0.17
rpoC 765775 c.2406C>T synonymous_variant 0.17
rpoC 765811 c.2442T>C synonymous_variant 0.18
rpoC 766111 c.2742G>A synonymous_variant 0.2
rpoC 767214 p.Ala1282Val missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 0.91
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776145 p.Ala779Val missense_variant 0.25
mmpL5 776393 p.Phe696Leu missense_variant 0.18
mmpL5 777993 p.Asn163Ile missense_variant 0.4
mmpS5 778508 p.Ala133Val missense_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303455 c.525C>T synonymous_variant 0.89
Rv1258c 1406218 p.Gly375Arg missense_variant 0.2
Rv1258c 1407466 c.-127_-126insA upstream_gene_variant 0.14
embR 1416222 p.Phe376Leu missense_variant 0.12
embR 1416232 c.1116T>C synonymous_variant 0.11
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417279 c.69C>T synonymous_variant 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472899 n.1054C>A non_coding_transcript_exon_variant 0.13
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.22
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.12
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.12
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.14
rrs 1473216 n.1371C>T non_coding_transcript_exon_variant 0.12
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.15
rpsA 1833941 p.Val134Ile missense_variant 0.4
tlyA 1917817 c.-122delC upstream_gene_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102891 p.Phe51Ser missense_variant 0.22
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167879 p.Ser912Arg missense_variant 0.2
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.36
PPE35 2169910 p.Asn235Tyr missense_variant 0.29
Rv1979c 2222155 p.Pro337Leu missense_variant 0.25
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223341 c.-177C>T upstream_gene_variant 0.33
pncA 2289278 c.-37A>G upstream_gene_variant 0.2
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2518376 p.Lys88* stop_gained 0.18
kasA 2518469 p.Ala119Thr missense_variant 0.13
kasA 2518926 p.Thr271Asn missense_variant 0.22
eis 2715555 c.-223G>T upstream_gene_variant 0.12
eis 2715570 c.-238C>T upstream_gene_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0
Rv2752c 3065305 p.Ala296Val missense_variant 0.75
Rv2752c 3065331 c.861C>T synonymous_variant 0.22
Rv2752c 3066223 c.-32G>C upstream_gene_variant 0.22
thyA 3074650 c.-179G>A upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087676 p.Pro286Gln missense_variant 0.14
fbiD 3339592 p.His159Tyr missense_variant 0.17
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448967 p.Gly155Asp missense_variant 0.18
Rv3083 3449000 p.Pro166Gln missense_variant 0.18
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
Rv3236c 3613234 c.-118G>A upstream_gene_variant 0.17
fbiA 3640528 c.-15G>A upstream_gene_variant 0.12
fbiB 3640575 c.-960C>A upstream_gene_variant 0.17
alr 3841546 c.-126C>A upstream_gene_variant 0.18
rpoA 3877770 c.738A>C synonymous_variant 0.33
rpoA 3878034 p.Glu158Asp missense_variant 0.12
rpoA 3878688 c.-181C>A upstream_gene_variant 0.2
clpC1 4039316 p.Glu463Asp missense_variant 0.18
clpC1 4039645 p.His354Asp missense_variant 0.22
clpC1 4039654 p.Thr351Ser missense_variant 0.25
clpC1 4039829 p.Leu292Ile missense_variant 0.14
clpC1 4040144 c.561G>C synonymous_variant 0.22
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240199 p.Ala113Ser missense_variant 0.18
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241288 p.Ile476Phe missense_variant 0.12
embA 4242436 c.-797G>T upstream_gene_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4245380 c.2148C>T synonymous_variant 0.14
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4246514 c.1A>G start_lost 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248915 p.Ala801Val missense_variant 0.13
aftB 4267873 p.Gln322* stop_gained 0.33
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ubiA 4269748 p.Asn29Ser missense_variant 0.2
ethA 4326012 p.Gly488Arg missense_variant 0.91
ethA 4326473 p.Pro334Leu missense_variant 0.12
ethR 4327051 c.-498G>A upstream_gene_variant 0.25
ethA 4327161 p.Ile105Val missense_variant 0.22
ethA 4328291 c.-818C>A upstream_gene_variant 0.17
whiB6 4338224 c.297delC frameshift_variant 0.19
whiB6 4338285 c.237C>T synonymous_variant 0.15
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
gid 4408095 c.108G>A synonymous_variant 0.22