TB-Profiler result

Run: SRR6896297
Summary

Run ID: SRR6896297

Sample name:

Date: 04-04-2023 18:01:34

Number of reads: 366898

Percentage reads mapped: 99.57

Strain: lineage3.1.2

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
lineage3 East-African-Indian CAS RD750 0.99
lineage3.1 East-African-Indian Non-CAS1-Delhi RD750 1.0
lineage3.1.2 East-African-Indian CAS;CAS2 RD750 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 5543 p.Gln102* stop_gained 0.12
gyrB 6173 p.Glu312* stop_gained 0.13
gyrB 6639 c.1405delA frameshift_variant 0.15
gyrA 7293 c.-9G>T upstream_gene_variant 0.13
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9113 c.1812C>A synonymous_variant 0.21
gyrA 9304 p.Gly668Asp missense_variant 1.0
gyrA 9356 c.2055G>T synonymous_variant 1.0
fgd1 491023 p.Tyr81His missense_variant 0.18
fgd1 491293 p.Pro171Ser missense_variant 0.29
fgd1 491342 p.Arg187Leu missense_variant 0.22
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575440 c.93C>A synonymous_variant 0.18
mshA 575588 p.Arg81Ser missense_variant 0.22
mshA 575747 p.Ala134Thr missense_variant 0.13
mshA 575981 p.Arg212Trp missense_variant 0.22
mshA 576169 c.822C>A synonymous_variant 0.2
mshA 576623 p.Ala426Thr missense_variant 0.15
ccsA 619978 p.Leu30Met missense_variant 0.18
ccsA 620337 c.447C>A synonymous_variant 0.29
ccsA 620605 c.719delT frameshift_variant 0.17
rpoB 759746 c.-61C>T upstream_gene_variant 1.0
rpoB 761877 p.Glu691* stop_gained 0.14
rpoC 762434 c.-936T>G upstream_gene_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763911 p.Leu181Pro missense_variant 0.12
rpoC 765772 c.2403C>T synonymous_variant 0.5
rpoC 766836 p.Val1156Ala missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776769 p.Ile571Thr missense_variant 0.17
mmpL5 777711 p.Gly257Val missense_variant 0.18
mmpL5 778612 c.-132C>T upstream_gene_variant 0.2
mmpR5 779473 p.Gly162* stop_gained 0.13
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781637 c.78C>A synonymous_variant 0.18
fbiC 1303266 c.336C>T synonymous_variant 0.22
fbiC 1303725 p.Glu265Asp missense_variant 0.14
fbiC 1304289 c.1359C>T synonymous_variant 0.25
fbiC 1305031 p.Gly701Ser missense_variant 0.18
fbiC 1305356 p.Gly809Asp missense_variant 0.2
Rv1258c 1406148 p.Pro398Leu missense_variant 0.12
Rv1258c 1406414 c.927G>A synonymous_variant 0.12
Rv1258c 1406444 c.897T>C synonymous_variant 0.14
Rv1258c 1406867 c.474G>T synonymous_variant 0.25
embR 1417141 c.207C>T synonymous_variant 0.18
embR 1417151 p.Ser66* stop_gained 0.18
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472557 n.712G>T non_coding_transcript_exon_variant 0.17
rrs 1473057 n.1212G>T non_coding_transcript_exon_variant 0.15
rrs 1473094 n.1249T>C non_coding_transcript_exon_variant 0.12
rrl 1473417 n.-241C>A upstream_gene_variant 0.29
rrl 1474300 n.643C>T non_coding_transcript_exon_variant 0.25
rrl 1474383 n.726G>T non_coding_transcript_exon_variant 0.15
rrl 1474486 n.829G>T non_coding_transcript_exon_variant 0.12
rrl 1474601 n.944C>A non_coding_transcript_exon_variant 0.13
rrl 1474738 n.1081G>T non_coding_transcript_exon_variant 0.13
fabG1 1673405 c.-35T>C upstream_gene_variant 0.17
inhA 1674837 c.636C>A synonymous_variant 0.12
inhA 1674948 p.Trp249* stop_gained 0.15
rpsA 1834920 p.Ala460Glu missense_variant 0.15
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101670 p.Ser458Ile missense_variant 0.14
katG 2153977 p.Gly712Val missense_variant 0.4
katG 2154617 p.Leu499Met missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155780 p.Gly111Val missense_variant 0.22
PPE35 2167676 c.2937C>A synonymous_variant 0.18
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168604 p.Pro670Leu missense_variant 1.0
PPE35 2169369 p.Gly415Val missense_variant 0.13
PPE35 2170266 p.Gly116Val missense_variant 0.2
PPE35 2170305 p.Ala103Val missense_variant 0.25
PPE35 2170789 c.-177C>A upstream_gene_variant 0.2
Rv1979c 2221756 c.1408delA frameshift_variant 0.11
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv1979c 2223351 c.-187C>A upstream_gene_variant 0.12
pncA 2289047 c.195C>T synonymous_variant 1.0
pncA 2289361 c.-120G>T upstream_gene_variant 0.12
pncA 2289365 c.-125delC upstream_gene_variant 1.0
pncA 2290072 c.-831T>C upstream_gene_variant 0.4
kasA 2518648 c.534C>T synonymous_variant 0.17
eis 2714616 c.717C>T synonymous_variant 0.15
eis 2714834 p.Arg167* stop_gained 0.25
eis 2714839 p.Leu165Trp missense_variant 0.33
eis 2714979 c.354G>A synonymous_variant 0.17
eis 2715219 c.114C>A synonymous_variant 0.13
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0
folC 2746215 p.Ser462Thr missense_variant 0.18
folC 2746268 p.Thr444Asn missense_variant 0.12
folC 2746660 c.938delT frameshift_variant 0.12
folC 2747025 p.Ala192Ser missense_variant 0.17
folC 2747390 p.Ala70Val missense_variant 0.14
folC 2747565 p.Gly12* stop_gained 0.18
pepQ 2859380 p.Gly347Trp missense_variant 0.13
pepQ 2859546 c.873T>G synonymous_variant 1.0
ribD 2986993 p.Gly52Val missense_variant 0.18
ribD 2987465 p.Asp209Glu missense_variant 0.15
Rv2752c 3065643 c.549C>A synonymous_variant 0.4
thyA 3073784 c.687delA frameshift_variant 0.17
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086846 c.27C>A synonymous_variant 0.15
ald 3087263 c.444C>T synonymous_variant 0.13
ald 3087324 p.Ala169Thr missense_variant 0.13
Rv3083 3449595 c.1092A>G synonymous_variant 0.15
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612070 c.1047G>T synonymous_variant 0.33
Rv3236c 3612213 p.Ala302Pro missense_variant 0.2
Rv3236c 3612260 p.Lys286Arg missense_variant 0.15
fbiB 3640776 c.-759C>A upstream_gene_variant 0.13
fbiB 3640857 c.-678G>C upstream_gene_variant 0.18
fbiB 3641748 p.Arg72* stop_gained 0.22
fbiB 3641949 p.Arg139Trp missense_variant 0.13
fbiB 3642532 p.Arg333His missense_variant 0.12
rpoA 3878078 p.Arg144Cys missense_variant 0.25
clpC1 4038230 p.Lys825Asn missense_variant 0.14
clpC1 4039455 p.Ala417Glu missense_variant 0.2
clpC1 4039725 p.Glu327Gly missense_variant 0.14
clpC1 4040375 c.330G>A synonymous_variant 0.29
clpC1 4040537 c.168G>A synonymous_variant 0.4
embC 4240107 p.Leu82Ser missense_variant 0.18
embC 4240527 c.673_675delAGC conservative_inframe_deletion 0.29
embC 4241344 c.1482G>T synonymous_variant 0.13
embC 4242075 p.Arg738Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243782 p.Gly184Trp missense_variant 0.18
embA 4244422 p.Glu397Gly missense_variant 0.2
embA 4244602 p.Ala457Val missense_variant 0.18
embB 4247557 c.1044G>T synonymous_variant 0.15
embB 4247601 p.Leu363Pro missense_variant 0.12
embB 4248386 p.Arg625Gly missense_variant 0.13
embB 4248443 p.Asn644Asp missense_variant 0.1
embB 4248883 c.2370C>A synonymous_variant 0.2
embB 4249307 p.Leu932Met missense_variant 0.5
aftB 4268614 p.Gly75Trp missense_variant 1.0
ubiA 4269920 c.-87G>A upstream_gene_variant 0.12
ethA 4326050 p.Asp475Gly missense_variant 0.18
ethA 4326181 p.Phe431Leu missense_variant 1.0
ethA 4327367 p.Glu36Gly missense_variant 0.17
ethR 4327708 p.Ala54Ser missense_variant 0.4
ethA 4328339 c.-866T>A upstream_gene_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407899 c.302_303delTT frameshift_variant 0.4