TB-Profiler result

Run: SRR6982530
Summary

Run ID: SRR6982530

Sample name:

Date: 04-04-2023 18:40:12

Number of reads: 440030

Percentage reads mapped: 96.36

Strain: lineage1.2.2.1

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 Indo-Oceanic EAI RD239 1.0
lineage1.2.2 Indo-Oceanic EAI1 RD239 1.0
lineage1.2.2.1 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 1472644 n.799C>T non_coding_transcript_exon_variant 0.11 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 5075 c.-165C>T upstream_gene_variant 1.0
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 491060 p.Met93Thr missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576484 c.1137C>A synonymous_variant 0.12
ccsA 620344 p.Ser152Pro missense_variant 0.11
ccsA 620659 p.Arg257Cys missense_variant 1.0
rpoC 762419 c.-951C>A upstream_gene_variant 0.12
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 765219 p.Glu617Gly missense_variant 0.13
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
rplC 800899 p.Ala31Thr missense_variant 1.0
embR 1417019 p.Cys110Tyr missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471842 n.-4T>G upstream_gene_variant 1.0
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.1
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.1
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.1
rrs 1472683 n.838T>C non_coding_transcript_exon_variant 0.1
rrs 1472686 n.841G>T non_coding_transcript_exon_variant 0.11
rrs 1472687 n.842A>T non_coding_transcript_exon_variant 0.11
rrs 1472692 n.847T>C non_coding_transcript_exon_variant 0.11
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.11
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.1
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.13
rrs 1473026 n.1181T>C non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.11
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.12
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.13
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.1
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.11
rrl 1474359 n.702C>G non_coding_transcript_exon_variant 0.11
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.11
rrl 1475747 n.2090A>G non_coding_transcript_exon_variant 0.12
rrl 1475757 n.2101_2104delACCC non_coding_transcript_exon_variant 0.12
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.12
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.12
rrl 1475766 n.2109G>C non_coding_transcript_exon_variant 0.12
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.12
rrl 1475781 n.2124T>C non_coding_transcript_exon_variant 0.14
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.12
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.12
rrl 1475883 n.2226A>C non_coding_transcript_exon_variant 0.12
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.12
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.1
rrl 1475916 n.2259C>T non_coding_transcript_exon_variant 0.13
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.13
rrl 1475945 n.2288C>A non_coding_transcript_exon_variant 0.13
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.13
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.14
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.14
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.14
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.13
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.13
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.13
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.12
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.12
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.14
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.22
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.19
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.17
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.1
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103173 c.-131C>A upstream_gene_variant 0.11
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
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
eis 2715247 p.Gly29Val missense_variant 0.13
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
folC 2746749 p.Gly284Arg missense_variant 0.13
Rv2752c 3065373 c.819A>G synonymous_variant 1.0
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 3474946 p.Pro314Ser missense_variant 0.12
fprA 3475123 p.Lys373Glu missense_variant 0.12
fprA 3475159 p.Asn385Asp missense_variant 1.0
fprA 3475339 p.Ala445Thr missense_variant 0.11
Rv3236c 3612068 p.Gly350Val missense_variant 0.14
fbiB 3642066 p.Gly178Cys missense_variant 0.17
ddn 3987052 p.Gly70Val missense_variant 1.0
clpC1 4040358 p.Gly116Val missense_variant 0.11
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4240750 c.888C>T synonymous_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 1.0
embB 4247646 p.Glu378Ala missense_variant 1.0
aftB 4267779 p.Ile353Thr missense_variant 1.0
aftB 4268594 c.243C>T synonymous_variant 0.2
ubiA 4269387 p.Glu149Asp missense_variant 1.0
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4326439 p.Asn345Lys missense_variant 1.0
ethR 4327450 c.-99G>A 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 4407660 c.543G>A synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 1.0