TB-Profiler result

Run: SRR4035748
Summary

Run ID: SRR4035748

Sample name:

Date: 04-04-2023 07:16:30

Number of reads: 1150350

Percentage reads mapped: 99.55

Strain: lineage4.1.2

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 1.0
lineage4.1.2 Euro-American T;H 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
gyrB 6371 p.Thr378Ala missense_variant 0.13
gyrA 7000 c.-302C>T upstream_gene_variant 0.13
gyrB 7025 p.Lys596Glu missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7672 p.Pro124Gln missense_variant 0.13
gyrA 8061 p.Arg254Cys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
fgd1 491729 p.Asp316Gly missense_variant 0.11
mshA 575636 p.Asp97Asn missense_variant 0.12
mshA 576275 p.Asp310Asn missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoB 760608 c.802C>T synonymous_variant 0.15
rpoB 760669 p.Thr288Met missense_variant 0.15
rpoB 760721 c.915C>T synonymous_variant 0.12
rpoB 760732 p.Lys309Arg missense_variant 0.12
rpoB 761424 p.Ser540Pro missense_variant 0.15
rpoB 761444 c.1638T>G synonymous_variant 0.15
rpoC 764263 c.894G>A synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776651 c.1830C>T synonymous_variant 0.13
mmpL5 776663 c.1818C>T synonymous_variant 0.14
mmpL5 777320 c.1161C>G synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473316 n.1473delG non_coding_transcript_exon_variant 0.18
rrl 1473454 n.-204A>T upstream_gene_variant 0.25
rrl 1476478 n.2821G>A non_coding_transcript_exon_variant 0.2
rrl 1476520 n.2863G>A non_coding_transcript_exon_variant 0.18
rpsA 1834237 c.696C>T synonymous_variant 0.2
rpsA 1834265 p.Trp242Arg missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101975 c.1067delC frameshift_variant 0.12
ndh 2102762 p.Leu94Pro missense_variant 0.12
ndh 2102771 c.271delC frameshift_variant 0.17
katG 2154332 p.Phe594Leu missense_variant 0.2
katG 2156013 c.99C>A synonymous_variant 0.14
katG 2156049 c.63C>G synonymous_variant 0.11
PPE35 2168372 c.2241G>A synonymous_variant 0.13
PPE35 2168713 p.Ala634Pro missense_variant 0.12
PPE35 2169119 c.1493delT frameshift_variant 0.18
PPE35 2170158 p.Ala152Gly missense_variant 0.11
Rv1979c 2222927 p.Ala80Thr missense_variant 0.2
Rv1979c 2223270 c.-106C>G upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290152 c.-911G>A upstream_gene_variant 0.14
kasA 2517934 c.-181A>T upstream_gene_variant 0.12
kasA 2517941 c.-174C>T upstream_gene_variant 0.12
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
ahpC 2726210 c.18T>C synonymous_variant 0.2
ahpC 2726263 p.Ser24Phe missense_variant 0.13
ahpC 2726331 p.Trp47Arg missense_variant 0.25
thyX 3067918 p.Gln10* stop_gained 0.18
thyX 3067932 p.Ala5Val missense_variant 0.14
thyX 3068125 c.-180G>T upstream_gene_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449456 p.Thr318Asn missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474076 p.Lys24Glu missense_variant 0.12
Rv3236c 3611974 c.1143A>C synonymous_variant 1.0
Rv3236c 3612329 p.Leu263Pro missense_variant 0.15
fbiA 3640628 p.Ala29Asp missense_variant 0.2
fbiB 3642691 p.Val386Asp missense_variant 0.17
panD 4044312 c.-32delC upstream_gene_variant 0.18
embC 4241378 p.Val506Ile missense_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embC 4242944 p.Asn1028Asp missense_variant 0.11
embA 4244199 p.Trp323Arg missense_variant 0.11
embB 4245527 c.-987C>T upstream_gene_variant 0.13
embB 4246521 p.Gln3Pro missense_variant 0.11
embB 4248751 c.2238C>G synonymous_variant 0.22
embB 4249527 p.Gly1005Asp missense_variant 0.12
embB 4249715 p.Asp1068His missense_variant 0.12
embB 4249723 c.3210G>C synonymous_variant 0.1
ethA 4326471 p.Ala335Ser missense_variant 0.17
ethA 4326638 p.Arg279Gln missense_variant 0.15
ethA 4327546 c.-74delC upstream_gene_variant 0.15
whiB6 4338595 c.-75delG upstream_gene_variant 1.0