TB-Profiler result

Run: SRR21677855
Summary

Run ID: SRR21677855

Sample name:

Date: 04-04-2023 02:48:30

Number of reads: 175205

Percentage reads mapped: 99.4

Strain: lineage4

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
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 6158 c.921delC frameshift_variant 0.5
gyrB 7083 p.Glu615Val missense_variant 0.22
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7806 p.Arg169Trp missense_variant 0.2
gyrA 8574 p.Leu425Ile missense_variant 0.2
gyrA 9342 p.Ile681Phe missense_variant 0.18
fgd1 490603 c.-180G>A upstream_gene_variant 0.25
fgd1 491126 p.Ala115Asp missense_variant 0.12
fgd1 491633 p.Trp284* stop_gained 0.2
mshA 575408 p.Gly21Cys missense_variant 0.4
mshA 576110 p.Ala255Thr missense_variant 0.18
mshA 576119 p.Ala258Ser missense_variant 0.18
mshA 576172 p.Gln275His missense_variant 0.29
mshA 576668 p.Tyr441Asn missense_variant 0.4
ccsA 619902 c.12G>T synonymous_variant 0.25
ccsA 620384 p.Pro165Leu missense_variant 0.33
rpoB 761348 c.1542C>A synonymous_variant 0.18
rpoB 762676 p.Leu957Gln missense_variant 0.18
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775681 p.Gly934* stop_gained 0.67
mmpL5 775863 p.Ala873Glu missense_variant 0.18
mmpL5 776788 p.Glu565* stop_gained 0.22
mmpL5 777020 c.1461G>T synonymous_variant 0.2
mmpL5 778726 c.-246T>C upstream_gene_variant 0.17
mmpL5 779061 c.-581G>A upstream_gene_variant 0.25
mmpR5 779204 p.Arg72Gln missense_variant 0.25
mmpL5 779421 c.-941T>C upstream_gene_variant 0.2
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781716 p.Ala53Ser missense_variant 0.22
fbiC 1305252 c.2322G>T synonymous_variant 0.2
fbiC 1305322 p.Val798Met missense_variant 0.25
Rv1258c 1406123 c.1218G>T synonymous_variant 0.17
embR 1416339 p.Thr337Ala missense_variant 0.29
embR 1417491 c.-144C>A upstream_gene_variant 0.17
embR 1417505 c.-158G>A upstream_gene_variant 0.17
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472030 n.185G>C non_coding_transcript_exon_variant 0.12
rrs 1472454 n.609C>A non_coding_transcript_exon_variant 0.12
rrs 1472714 n.872_873delCC non_coding_transcript_exon_variant 0.22
rrs 1472961 n.1116T>C non_coding_transcript_exon_variant 0.22
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475152 n.1495G>A non_coding_transcript_exon_variant 0.18
rrl 1475951 n.2294G>T non_coding_transcript_exon_variant 0.25
rrl 1476012 n.2355T>C non_coding_transcript_exon_variant 0.13
rrl 1476499 n.2842T>A non_coding_transcript_exon_variant 0.25
fabG1 1673233 c.-207T>G upstream_gene_variant 1.0
fabG1 1674068 p.Arg210Leu missense_variant 0.33
fabG1 1674071 p.Val211Asp missense_variant 0.33
tlyA 1917794 c.-146C>A upstream_gene_variant 0.14
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918120 p.Ala61Ser missense_variant 0.33
tlyA 1918362 c.423G>C synonymous_variant 0.29
ndh 2103096 c.-54G>T upstream_gene_variant 0.67
katG 2154246 p.Pro622Arg missense_variant 0.29
katG 2155056 p.Gln352His missense_variant 0.22
PPE35 2168149 p.Pro822Ser missense_variant 1.0
PPE35 2169648 p.Phe322Tyr missense_variant 0.5
Rv1979c 2223239 c.-75G>A upstream_gene_variant 0.25
Rv1979c 2223258 c.-94T>A upstream_gene_variant 0.29
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518759 c.645C>T synonymous_variant 0.29
eis 2714177 p.Leu386Ile missense_variant 0.22
eis 2714261 p.Ser358Cys missense_variant 0.2
ahpC 2726039 c.-154C>A upstream_gene_variant 0.17
ahpC 2726122 c.-71T>G upstream_gene_variant 0.14
folC 2746245 p.Ala452Ser missense_variant 0.22
thyA 3074054 c.418C>A synonymous_variant 0.22
ald 3086851 c.33dupC frameshift_variant 0.17
ald 3087819 c.1000C>A synonymous_variant 0.5
fprA 3473860 c.-147G>A upstream_gene_variant 0.11
fprA 3474624 c.618G>A synonymous_variant 0.18
fbiB 3641223 c.-312C>T upstream_gene_variant 0.4
fbiB 3641543 c.9C>A synonymous_variant 0.2
fbiB 3641817 p.Thr95Ala missense_variant 0.18
alr 3841475 c.-55C>G upstream_gene_variant 0.14
clpC1 4038278 c.2427T>A synonymous_variant 0.5
clpC1 4038534 p.Arg724Leu missense_variant 0.33
clpC1 4038936 p.Thr590Ile missense_variant 0.33
clpC1 4039155 p.Arg517Gln missense_variant 0.2
clpC1 4039244 c.1461G>A synonymous_variant 0.13
clpC1 4039729 p.Asp326Asn missense_variant 1.0
clpC1 4040493 p.Gln71Leu missense_variant 0.12
panD 4044329 c.-48C>T upstream_gene_variant 0.25
embC 4240239 p.Ala126Asp missense_variant 0.29
embC 4240299 p.Gln146Pro missense_variant 0.29
embC 4241243 p.His461Tyr missense_variant 0.17
embC 4241431 c.1569C>T synonymous_variant 0.33
embC 4242317 p.Glu819Lys missense_variant 0.29
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4244565 p.Arg445Cys missense_variant 0.2
embA 4245678 p.Lys816Glu missense_variant 0.25
embA 4246386 p.Arg1052Cys missense_variant 0.5
embB 4246718 p.Ala69Thr missense_variant 0.4
embB 4248480 p.Phe656Tyr missense_variant 0.22
embB 4248605 p.Leu698Met missense_variant 0.22
ubiA 4269022 p.Ala271Val missense_variant 0.25
ethA 4326533 p.Thr314Asn missense_variant 0.14
ethA 4327325 p.Tyr50Cys missense_variant 0.17
ethA 4327893 c.-420C>G upstream_gene_variant 0.17
ethA 4328237 c.-764C>T upstream_gene_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338606 c.-85G>A upstream_gene_variant 0.4