TB-Profiler result

Run: SRR6982301
Summary

Run ID: SRR6982301

Sample name:

Date: 04-04-2023 18:33:17

Number of reads: 258607

Percentage reads mapped: 99.51

Strain: lineage4.1.1

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.99
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9403 p.Gln701Arg missense_variant 0.17
gyrA 9650 c.2349G>C synonymous_variant 0.13
ccsA 620748 c.858T>G synonymous_variant 0.33
rpoC 763851 p.Ala161Asp missense_variant 0.4
rpoC 763854 p.Val162Asp missense_variant 0.4
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765832 p.Lys821Asn missense_variant 0.12
rpoC 765990 p.Thr874Asn missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775646 c.2835A>G synonymous_variant 0.2
mmpL5 775756 c.2724delC frameshift_variant 0.25
mmpL5 777354 p.Val376Gly missense_variant 0.25
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781839 p.Arg94Ser missense_variant 0.14
fbiC 1303581 c.651G>T synonymous_variant 0.15
fbiC 1304785 p.Arg619Ser missense_variant 0.13
Rv1258c 1407295 p.Thr16Ala missense_variant 0.13
embR 1416447 p.Tyr301His missense_variant 0.12
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.12
rrs 1473158 n.1313T>A non_coding_transcript_exon_variant 0.18
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.12
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.12
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.12
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.13
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.13
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.13
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.12
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.12
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.12
rrl 1476302 n.2645G>A 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 0.12
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.12
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.12
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.14
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.15
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.15
rpsA 1834803 p.Ala421Asp missense_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103225 c.-183A>C upstream_gene_variant 0.33
Rv1979c 2223071 p.Ile32Val missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065657 p.Asp179Tyr missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448496 c.-8C>A upstream_gene_variant 0.2
Rv3083 3449822 p.Asn440Ser missense_variant 0.12
Rv3083 3449935 p.Ile478Val missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3641447 p.Thr302Met missense_variant 1.0
alr 3840651 c.769delG frameshift_variant 0.17
rpoA 3877553 p.Glu319Lys missense_variant 1.0
clpC1 4039729 p.Asp326His missense_variant 0.17
panD 4044022 p.Leu87Pro missense_variant 0.17
embC 4239973 c.111T>G synonymous_variant 0.2
embC 4240897 c.1035C>G synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ubiA 4269475 p.Leu120Pro missense_variant 0.2
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407671 p.Met178Leu missense_variant 0.22