TB-Profiler result

Run: SRR4035623
Summary

Run ID: SRR4035623

Sample name:

Date: 04-04-2023 07:13:19

Number of reads: 547732

Percentage reads mapped: 99.69

Strain: lineage4.3.4.2.1

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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.2 Euro-American (LAM) LAM1;LAM4;LAM11 RD174 1.0
lineage4.3.4.2.1 Euro-American (LAM) LAM11 RD174 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
gyrB 5088 c.-151delA upstream_gene_variant 0.15
gyrB 5560 c.321C>T synonymous_variant 0.18
gyrB 5770 c.531C>T synonymous_variant 0.22
gyrB 6140 p.Val301Leu missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8478 c.1178_1179dupGC frameshift_variant 0.13
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620420 p.Ser177Leu missense_variant 0.17
rpoB 760305 c.503_504delTG frameshift_variant 0.1
rpoB 761556 c.1752dupC frameshift_variant 0.25
rpoC 764223 c.858delG frameshift_variant 0.12
rpoC 764995 c.1626C>G synonymous_variant 1.0
rpoC 765181 c.1812G>A synonymous_variant 0.5
rpoC 766144 c.2775G>T synonymous_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777501 p.Thr327Ile missense_variant 0.17
mmpR5 778298 c.-692C>T upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781904 c.345C>T synonymous_variant 0.21
fbiC 1304673 c.1743C>A synonymous_variant 0.13
Rv1258c 1407129 p.Arg71His missense_variant 0.2
Rv1258c 1407315 c.25delG frameshift_variant 0.33
embR 1417150 c.198G>T synonymous_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472248 n.403G>A non_coding_transcript_exon_variant 0.15
rrs 1472597 n.752G>C non_coding_transcript_exon_variant 0.14
rrs 1473362 n.1517C>A non_coding_transcript_exon_variant 0.12
rrl 1475136 n.1479G>A non_coding_transcript_exon_variant 0.25
rrl 1476155 n.2498C>T non_coding_transcript_exon_variant 0.2
rrl 1476766 n.3109C>T non_coding_transcript_exon_variant 0.17
inhA 1674687 c.487_488delGT frameshift_variant 0.11
rpsA 1834111 p.Trp190Cys missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101935 p.Met370Val missense_variant 0.13
katG 2155698 c.414C>T synonymous_variant 0.25
katG 2155767 c.345C>A synonymous_variant 0.33
katG 2156216 c.-105C>T upstream_gene_variant 0.18
PPE35 2168429 c.2184G>T synonymous_variant 0.17
PPE35 2168831 c.1782C>A synonymous_variant 0.22
PPE35 2169252 p.Ala454Val missense_variant 0.33
PPE35 2169320 p.Leu431Phe missense_variant 0.4
PPE35 2169603 p.Gly337Asp missense_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726192 c.-1C>A upstream_gene_variant 0.14
ribD 2986923 p.Pro29Thr missense_variant 0.12
Rv2752c 3064706 p.Gly496Cys missense_variant 0.29
Rv2752c 3067078 c.-887T>C upstream_gene_variant 0.17
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086677 c.-143A>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086934 p.Ala39Ser missense_variant 0.2
ald 3086971 p.Lys51Met missense_variant 0.22
ald 3087186 p.Ala123Thr missense_variant 0.18
ald 3087525 p.Ile236Val missense_variant 0.22
Rv3083 3449277 c.774C>T synonymous_variant 0.25
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
Rv3236c 3612230 p.Ala296Val missense_variant 0.15
fbiA 3640613 p.Gly24Asp missense_variant 0.14
fbiA 3640910 c.373delC frameshift_variant 0.5
alr 3840719 c.702A>G synonymous_variant 1.0
alr 3841593 c.-174delT upstream_gene_variant 0.25
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040501 c.203dupG frameshift_variant 0.17
embC 4240323 p.Arg154Gln missense_variant 0.25
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244709 p.Ile493Val missense_variant 0.13
embB 4249332 p.Pro940Leu missense_variant 0.67
embB 4249622 p.Leu1037Phe missense_variant 0.15
aftB 4267035 c.1801dupC frameshift_variant 0.22
aftB 4267299 p.Pro513Gln missense_variant 0.15
aftB 4268122 p.Thr239Ala missense_variant 0.11
ubiA 4269077 p.Ile253Phe missense_variant 0.17
ethA 4326732 p.Ala248Thr missense_variant 0.17
ethA 4328268 c.-795G>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0