TB-Profiler result

Run: SRR20995191
Summary

Run ID: SRR20995191

Sample name:

Date: 03-04-2023 22:42:44

Number of reads: 947878

Percentage reads mapped: 81.94

Strain: lineage4.4.1.1

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
lineage4.4 Euro-American S;T None 0.96
lineage4.4.1 Euro-American (S-type) S;T None 1.0
lineage4.4.1.1 Euro-American S;Orphans 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
mshA 576493 c.1146C>T synonymous_variant 0.18
ccsA 620167 p.Ala93Ser missense_variant 0.13
rpoB 762058 p.Ile751Asn missense_variant 0.17
rpoC 763488 p.Lys40Arg missense_variant 0.17
rpoC 765540 p.Ala724Asp missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775813 p.Phe890Val missense_variant 0.14
mmpL5 775817 c.2664T>C synonymous_variant 0.12
mmpL5 775820 c.2661G>A synonymous_variant 0.22
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781831 p.Pro91His missense_variant 0.29
fbiC 1303016 p.Val29Gly missense_variant 0.25
fbiC 1304826 c.1900delT frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472954 n.1110delC non_coding_transcript_exon_variant 0.24
rrs 1472958 n.1113_1114insC non_coding_transcript_exon_variant 0.24
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.19
rrs 1472986 n.1141_1142insA non_coding_transcript_exon_variant 0.14
rrs 1472989 n.1145delA non_coding_transcript_exon_variant 0.14
rrs 1472996 n.1151T>C non_coding_transcript_exon_variant 0.14
rrs 1473053 n.1208T>C non_coding_transcript_exon_variant 0.13
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.13
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.13
rrs 1473100 n.1255G>A non_coding_transcript_exon_variant 0.2
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.14
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.19
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.2
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.25
rrs 1473122 n.1277T>A non_coding_transcript_exon_variant 0.17
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.23
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrl 1474552 n.895C>T non_coding_transcript_exon_variant 0.15
rrl 1474558 n.901G>A non_coding_transcript_exon_variant 0.15
rrl 1474582 n.925T>A non_coding_transcript_exon_variant 0.13
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.17
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.17
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.17
rrl 1474639 n.982G>T non_coding_transcript_exon_variant 0.15
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.15
rrl 1474651 n.995delT non_coding_transcript_exon_variant 0.12
rrl 1474662 n.1005C>T non_coding_transcript_exon_variant 0.12
rrl 1474664 n.1007G>T non_coding_transcript_exon_variant 0.12
rrl 1474666 n.1009T>G non_coding_transcript_exon_variant 0.12
rrl 1474670 n.1013C>G non_coding_transcript_exon_variant 0.12
rrl 1474672 n.1015C>T non_coding_transcript_exon_variant 0.12
rrl 1474675 n.1018C>T non_coding_transcript_exon_variant 0.12
rrl 1474676 n.1019T>C non_coding_transcript_exon_variant 0.12
rrl 1474677 n.1020A>G non_coding_transcript_exon_variant 0.12
rrl 1474679 n.1022G>C non_coding_transcript_exon_variant 0.12
rrl 1474684 n.1027T>C non_coding_transcript_exon_variant 0.12
rrl 1474687 n.1030C>A non_coding_transcript_exon_variant 0.11
rrl 1474688 n.1031G>A non_coding_transcript_exon_variant 0.11
rrl 1474707 n.1051_1052delCG non_coding_transcript_exon_variant 0.13
rrl 1474711 n.1055_1056insCAAG non_coding_transcript_exon_variant 0.13
fabG1 1673357 c.-83G>A upstream_gene_variant 0.15
fabG1 1673359 c.-81T>C upstream_gene_variant 0.15
fabG1 1673361 c.-79C>G upstream_gene_variant 0.15
fabG1 1673380 c.-60C>G upstream_gene_variant 0.2
rpsA 1833432 c.-110C>T upstream_gene_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101840 c.1203G>A synonymous_variant 0.2
ndh 2102990 p.Val18Ala missense_variant 1.0
PPE35 2169840 p.Gly258Asp missense_variant 1.0
PPE35 2169902 c.711G>C synonymous_variant 0.12
PPE35 2170048 p.Leu189Val missense_variant 0.49
PPE35 2170053 p.Thr187Ser missense_variant 0.5
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2519128 c.1014G>C synonymous_variant 0.17
kasA 2519131 c.1017G>C synonymous_variant 0.17
thyX 3067277 c.669C>A synonymous_variant 0.29
thyA 3074514 c.-43T>C upstream_gene_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448425 c.-79A>T upstream_gene_variant 0.13
Rv3083 3448608 c.105G>A synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612155 p.Arg321Leu missense_variant 1.0
Rv3236c 3612469 p.Glu216Asp missense_variant 0.15
Rv3236c 3612665 p.Val151Ala missense_variant 1.0
rpoA 3878282 p.Ile76Val missense_variant 0.13
clpC1 4038902 p.Tyr601* stop_gained 0.18
clpC1 4040380 c.325T>C synonymous_variant 0.17
clpC1 4040381 p.Ile108Leu missense_variant 0.17
panD 4044394 c.-113C>T upstream_gene_variant 0.14
embC 4239693 c.-170G>A upstream_gene_variant 0.13
embC 4240648 c.786C>T synonymous_variant 0.23
embC 4242220 c.2358A>C synonymous_variant 0.5
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244843 c.1611G>C synonymous_variant 0.2
embA 4244850 p.Arg540Gly missense_variant 0.13
embB 4246544 p.Thr11Pro missense_variant 0.23
embB 4246548 p.Pro12Gln missense_variant 0.29
embB 4246555 c.42G>C synonymous_variant 0.23
embB 4246556 p.Ala15Pro missense_variant 0.23
embB 4248495 p.Pro661Gln missense_variant 0.12
embB 4248539 p.Phe676Ile missense_variant 0.14
ethR 4326961 c.-588G>C upstream_gene_variant 0.17
ethR 4326964 c.-585G>A upstream_gene_variant 0.17
ethR 4326970 c.-579G>T upstream_gene_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0