TB-Profiler result

Run: SRR1003105
Summary

Run ID: SRR1003105

Sample name:

Date: 02-04-2023 14:20:15

Number of reads: 6822594

Percentage reads mapped: 96.58

Strain:

Drug-resistance: Pre-XDR-TB

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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
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
gyrB 6738 p.Thr500Asn missense_variant 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761125 p.Leu440Pro missense_variant 0.25 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2288959 c.282delC frameshift_variant 0.75 pyrazinamide
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
folC 2747471 p.Ile43Ser missense_variant 1.0 para-aminosalicylic_acid
embB 4247469 p.Tyr319Ser missense_variant 0.91 ethambutol
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 5555 p.Gly106Ser missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 0.88
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 576137 p.Asp264Asn missense_variant 0.22
ccsA 620537 c.653_655dupGGC disruptive_inframe_insertion 0.12
rpoB 759738 c.-69G>T upstream_gene_variant 0.39
rpoB 761165 c.1362delC frameshift_variant 0.28
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763888 c.519G>A synonymous_variant 0.33
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 777886 p.Ala199Thr missense_variant 0.57
mmpS5 779615 c.-710C>G upstream_gene_variant 0.91
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304915 p.Asp662Gly missense_variant 0.33
Rv1258c 1406257 c.1083_1084insC frameshift_variant 0.25
Rv1258c 1406261 c.1080C>T synonymous_variant 0.29
Rv1258c 1406270 p.Tyr357* stop_gained 0.25
Rv1258c 1406810 c.531C>A synonymous_variant 0.5
embR 1416485 c.862delG frameshift_variant 0.15
embR 1416491 p.Gln286Arg missense_variant 0.15
embR 1416813 p.Glu179Lys missense_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.19
rrs 1472223 n.378C>G non_coding_transcript_exon_variant 0.33
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33
rrs 1472228 n.383G>C non_coding_transcript_exon_variant 0.33
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.29
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.33
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.25
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.25
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.13
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.14
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.2
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.14
rrl 1475132 n.1475T>A non_coding_transcript_exon_variant 0.25
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.22
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.33
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.45
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.5
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.27
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.16
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.2
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.39
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.27
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.18
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.5
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.29
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.29
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.29
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.29
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.29
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.22
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.22
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.22
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.22
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.2
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.18
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.25
rrl 1476572 n.2915G>T non_coding_transcript_exon_variant 0.25
rrl 1476573 n.2916A>G non_coding_transcript_exon_variant 0.25
inhA 1673922 c.-280T>A upstream_gene_variant 0.5
fabG1 1673941 c.505delC frameshift_variant 0.23
rpsA 1834177 c.636A>C synonymous_variant 0.91
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102537 p.Lys169Arg missense_variant 0.25
katG 2154477 c.1632_1634delCGT disruptive_inframe_deletion 0.29
katG 2154485 p.Leu543Ile missense_variant 0.25
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154978 c.1134G>T synonymous_variant 0.22
katG 2155563 p.Phe183Leu missense_variant 1.0
katG 2155742 p.Gly124Ser missense_variant 1.0
PPE35 2169643 p.Ala324Thr missense_variant 0.38
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288724 p.Glu173Ala missense_variant 1.0
kasA 2519264 p.Val384Phe missense_variant 0.17
eis 2714368 p.Glu322Gly missense_variant 0.19
eis 2714529 c.804C>A synonymous_variant 0.59
eis 2714707 p.Gly209Val missense_variant 0.35
eis 2714710 p.Pro208Leu missense_variant 0.33
ahpC 2725942 c.-251C>T upstream_gene_variant 0.4
ahpC 2726341 p.Val50Gly missense_variant 0.22
ribD 2987313 p.Leu159Ile missense_variant 0.18
Rv2752c 3065436 c.756A>T synonymous_variant 0.71
Rv2752c 3067014 c.-823G>T upstream_gene_variant 0.2
Rv2752c 3067038 c.-847G>C upstream_gene_variant 0.29
thyA 3073806 c.666C>G synonymous_variant 0.4
ald 3087199 p.Leu127Gln missense_variant 0.5
ald 3087321 p.Pro168Ser missense_variant 0.33
fbiD 3339300 c.184delA frameshift_variant 0.33
Rv3083 3448894 p.Tyr131Asn missense_variant 0.17
Rv3083 3449606 p.Pro368Gln missense_variant 0.52
fprA 3473971 c.-36T>C upstream_gene_variant 0.4
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.71
Rv3236c 3612512 p.Trp202* stop_gained 0.2
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640452 c.-91C>T upstream_gene_variant 0.22
rpoA 3878123 p.Asn129Asp missense_variant 0.27
rpoA 3878124 c.384G>C synonymous_variant 0.27
rpoA 3878551 c.-44C>A upstream_gene_variant 0.5
clpC1 4039939 p.Val256Leu missense_variant 0.45
clpC1 4039941 p.Leu255Pro missense_variant 0.45
clpC1 4040272 p.Tyr145His missense_variant 0.17
clpC1 4040631 p.His25Leu missense_variant 0.13
clpC1 4040636 p.Leu23Pro missense_variant 0.15
clpC1 4040639 p.Met22Val missense_variant 0.13
embC 4240081 c.219G>T synonymous_variant 0.12
embC 4240301 p.Val147Leu missense_variant 0.13
embC 4242381 p.Pro840His missense_variant 0.44
embC 4242384 p.Tyr841Cys missense_variant 0.5
embC 4242389 c.2528delT frameshift_variant 0.44
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245446 c.2214C>T synonymous_variant 0.12
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327465 p.Glu3Asp missense_variant 0.67
ethA 4327501 c.-28C>A upstream_gene_variant 1.0
ethR 4327894 p.Ser116Pro missense_variant 1.0
ethA 4328296 c.-823C>G upstream_gene_variant 0.13
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407634 p.Thr190Lys missense_variant 0.15
gid 4407927 p.Glu92Asp missense_variant 0.96