TB-Profiler result

Run: ERR6336782

Summary

Run ID: ERR6336782

Sample name:

Date: 02-04-2023 02:03:07

Number of reads: 191025

Percentage reads mapped: 99.18

Strain:

Drug-resistance: Other


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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
lineage1.2.1.2 Indo-Oceanic NA RD239 1.0
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
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
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 490715 c.-68A>G upstream_gene_variant 0.67
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575316 c.-32C>T upstream_gene_variant 0.22
mshA 575368 c.21T>C synonymous_variant 1.0
mshA 576293 p.Ala316Thr missense_variant 0.29
ccsA 620273 p.Val128Ala missense_variant 0.33
ccsA 620539 c.649C>A synonymous_variant 0.33
ccsA 620774 p.Ile295Thr missense_variant 0.4
rpoB 760171 p.Thr122Arg missense_variant 0.25
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763531 c.162G>C synonymous_variant 1.0
rpoC 763654 c.285C>T synonymous_variant 0.22
rpoC 764758 c.1389C>T synonymous_variant 0.18
rpoC 764976 c.1608delC frameshift_variant 0.5
mmpL5 775587 c.2894G>A splice_region_variant&stop_retained_variant 0.29
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775687 p.Leu932Phe missense_variant 0.5
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776146 p.Ala779Ser missense_variant 0.15
mmpL5 776164 p.Thr773Ala missense_variant 0.13
mmpL5 776846 c.1635G>A synonymous_variant 0.33
mmpS5 779612 c.-707G>A upstream_gene_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303258 p.Val110Leu missense_variant 0.29
fbiC 1303301 p.Glu124Gly missense_variant 0.33
fbiC 1303620 c.690C>T synonymous_variant 0.5
fbiC 1304924 p.Pro665Arg missense_variant 0.33
Rv1258c 1407284 c.57G>A synonymous_variant 0.29
Rv1258c 1407473 c.-133C>T upstream_gene_variant 0.29
embR 1416447 p.Tyr301His missense_variant 0.4
embR 1417019 p.Cys110Tyr missense_variant 1.0
embR 1417145 p.Ala68Val missense_variant 0.2
atpE 1460907 c.-138T>C upstream_gene_variant 1.0
atpE 1461185 c.141G>C synonymous_variant 0.67
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472056 n.211G>A non_coding_transcript_exon_variant 0.25
rrs 1472339 n.494C>T non_coding_transcript_exon_variant 0.29
rrs 1472750 n.905C>T non_coding_transcript_exon_variant 0.14
rrl 1474732 n.1075A>G non_coding_transcript_exon_variant 1.0
rrl 1475585 n.1928T>C non_coding_transcript_exon_variant 0.14
rpsA 1833673 c.132C>T synonymous_variant 0.25
rpsA 1834023 p.Leu161Pro missense_variant 0.5
tlyA 1917825 c.-115G>A upstream_gene_variant 0.5
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102949 p.Lys32* stop_gained 0.4
katG 2154037 p.Ser692Asn missense_variant 0.29
katG 2155260 c.852C>T synonymous_variant 0.33
katG 2156385 c.-274C>A upstream_gene_variant 0.29
katG 2156412 c.-301C>T upstream_gene_variant 0.29
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167948 c.2664delC frameshift_variant 0.4
PPE35 2169497 p.Phe372Leu missense_variant 0.18
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289940 c.-699C>T upstream_gene_variant 0.4
kasA 2518132 c.18C>T synonymous_variant 1.0
kasA 2519048 p.Gly312Ser missense_variant 1.0
eis 2714565 c.768G>A synonymous_variant 0.29
ahpC 2725930 c.-263C>T upstream_gene_variant 0.33
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726067 c.-126C>T upstream_gene_variant 0.15
ahpC 2726096 c.-97A>G upstream_gene_variant 0.11
ahpC 2726162 c.-31T>C upstream_gene_variant 0.11
folC 2746171 c.1428G>A synonymous_variant 0.33
folC 2746582 c.1017G>A synonymous_variant 0.25
folC 2747001 p.Asp200His missense_variant 0.12
pepQ 2860377 c.42C>T synonymous_variant 0.25
Rv2752c 3065828 p.Thr122Ala missense_variant 0.2
thyX 3067555 p.Ile131Val missense_variant 0.22
thyX 3067568 c.378C>T synonymous_variant 0.22
thyX 3067571 c.375C>T synonymous_variant 0.2
thyX 3067850 c.96A>G synonymous_variant 0.25
thyX 3067944 p.Val1Gly missense_variant 0.33
thyA 3074025 c.447C>T synonymous_variant 0.25
thyA 3074576 c.-105C>T upstream_gene_variant 0.33
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087476 c.657C>T synonymous_variant 0.22
ald 3087896 c.1077G>A synonymous_variant 0.67
fbiD 3339417 c.300A>G synonymous_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 1.0
Rv3083 3448796 p.Ile98Thr missense_variant 0.25
Rv3083 3449111 p.Ser203Asn missense_variant 0.22
Rv3083 3449488 p.Ile329Val missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474381 c.375C>T synonymous_variant 0.29
fprA 3474597 c.591C>A synonymous_variant 1.0
fprA 3474675 c.669G>A synonymous_variant 0.29
fprA 3475159 p.Asn385Asp missense_variant 1.0
whiB7 3568488 c.191delG frameshift_variant 1.0
Rv3236c 3612777 p.Asp114Asn missense_variant 0.33
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0
fbiA 3641104 p.Val188Phe missense_variant 1.0
fbiB 3642723 p.Trp397Arg missense_variant 0.25
alr 3841169 c.252C>T synonymous_variant 0.33
ddn 3986856 p.Pro5Ala missense_variant 0.13
ddn 3986862 p.Arg7Trp missense_variant 0.15
clpC1 4040372 c.332delG frameshift_variant 0.18
clpC1 4040517 p.Val63Ala missense_variant 1.0
clpC1 4040704 c.1A>T initiator_codon_variant 0.4
panD 4044095 p.Glu63Lys missense_variant 0.2
panD 4044324 c.-43C>T upstream_gene_variant 0.29
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embC 4241706 p.Ser615Leu missense_variant 0.25
embC 4241718 p.Arg619Gln missense_variant 0.22
embA 4242298 c.-935C>T upstream_gene_variant 0.22
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242679 c.-554C>T upstream_gene_variant 0.33
embC 4243020 p.Trp1053Leu missense_variant 0.5
embA 4244420 c.1188G>C synonymous_variant 1.0
embA 4245811 p.Pro860Leu missense_variant 0.4
embA 4246233 p.Glu1001Lys missense_variant 0.2
embB 4247578 c.1065G>A synonymous_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4248509 p.Ile666Val missense_variant 0.33
embB 4248560 p.Ala683Ser missense_variant 0.29
embB 4248745 c.2232C>T synonymous_variant 0.33
embB 4248815 p.Asp768Asn missense_variant 0.33
embB 4249779 p.Trp1089* stop_gained 0.33
aftB 4267670 c.1167G>A synonymous_variant 0.4
aftB 4268053 p.Arg262Gly missense_variant 0.29
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethR 4327012 c.-537C>T upstream_gene_variant 0.33
whiB6 4338361 p.Arg54Gln missense_variant 1.0
whiB6 4338569 c.-48A>G upstream_gene_variant 0.17
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 4407680 p.Arg175Trp missense_variant 0.33
gid 4407791 p.Ala138Ser missense_variant 0.33
gid 4407873 c.330G>T synonymous_variant 1.0
gid 4407880 p.Leu108Pro missense_variant 0.29