TB-Profiler result

Run: SRR1003100
Summary

Run ID: SRR1003100

Sample name:

Date: 02-04-2023 14:21:45

Number of reads: 14778811

Percentage reads mapped: 97.56

Strain: lineage2.2.1

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
lineage2 East-Asian Beijing RD105 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.98
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 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
gyrA 7570 p.Ala90Val missense_variant 0.86 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761101 p.Gln432Leu missense_variant 0.92 rifampicin
rpoB 761131 p.Gly442Glu missense_variant 0.94 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.83 isoniazid, ethionamide
katG 2155258 p.Gly285Asp missense_variant 0.97 isoniazid
pncA 2288930 p.Ser104Arg missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
ethA 4326980 p.Gln165Pro missense_variant 0.93 ethionamide
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 6328 p.Ser363Arg missense_variant 0.12
gyrB 6778 p.Ile513Met missense_variant 0.17
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 0.86
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575463 p.Ser39Leu missense_variant 0.29
ccsA 620444 p.Val185Ala missense_variant 0.32
rpoB 760001 c.195C>G synonymous_variant 0.24
rpoB 760086 c.280_281delTCinsAG synonymous_variant 0.22
rpoB 760095 p.Met97Val missense_variant 0.2
rpoB 761783 c.1977C>A synonymous_variant 0.18
rpoB 761968 p.Glu721Val missense_variant 0.27
rpoC 763031 c.-339T>C upstream_gene_variant 0.95
rpoC 764547 c.1178_1179insC frameshift_variant 0.32
rpoC 764553 p.Gly395Val missense_variant 0.32
rpoC 765240 p.Arg624Leu missense_variant 0.15
rpoC 765410 p.Tyr681Asp missense_variant 0.12
rpoC 766269 p.Thr967Met missense_variant 0.17
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775875 p.Gly869Asp missense_variant 0.33
mmpL5 775884 p.Ile866Ser missense_variant 0.26
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776743 p.Pro580Ser missense_variant 0.2
mmpR5 779063 p.Gly25Ala missense_variant 0.22
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801346 c.542delT frameshift_variant 0.15
fbiC 1304347 p.Trp473Arg missense_variant 0.42
fbiC 1304352 p.Glu474Asp missense_variant 0.3
fbiC 1305372 c.2442G>A synonymous_variant 0.5
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1416510 c.837delG frameshift_variant 0.22
embR 1416858 c.489delC frameshift_variant 0.4
rrs 1471659 n.-187C>T upstream_gene_variant 0.97
rrs 1471771 n.-75C>G upstream_gene_variant 0.19
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.13
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.2
rrl 1473893 n.236T>C non_coding_transcript_exon_variant 1.0
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.21
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.26
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.32
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.29
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.17
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.28
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.29
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.23
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.23
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.17
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.18
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.16
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.15
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.15
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.16
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.17
fabG1 1673296 c.-144T>G upstream_gene_variant 0.4
rpsA 1833818 p.Lys93Glu missense_variant 0.85
rpsA 1834177 c.636A>C synonymous_variant 0.89
rpsA 1834197 p.Ile219Thr missense_variant 0.13
rpsA 1834200 p.Val220Ala missense_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102351 p.Arg231Leu missense_variant 0.47
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2154978 c.1134G>A synonymous_variant 0.18
katG 2155126 p.Asp329Ala missense_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168913 p.Pro567Gln missense_variant 0.17
PPE35 2169687 p.Ile309Thr missense_variant 0.11
Rv1979c 2222617 c.547delT frameshift_variant 0.22
Rv1979c 2222798 p.Pro123Ala missense_variant 0.14
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289392 c.-151T>A upstream_gene_variant 0.17
kasA 2518798 c.684G>A synonymous_variant 0.18
eis 2714798 p.Tyr179Asn missense_variant 0.44
eis 2715329 p.Thr2Ala missense_variant 1.0
folC 2747172 p.Gly143Ser missense_variant 0.18
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
ribD 2986842 p.Pro2Ser missense_variant 1.0
Rv2752c 3064568 p.Gly542Trp missense_variant 0.18
Rv2752c 3065892 c.299_300insG frameshift_variant 0.14
Rv2752c 3066321 c.-130C>G upstream_gene_variant 0.67
thyX 3067535 c.411C>T synonymous_variant 0.22
thyA 3074105 p.Pro123Ser missense_variant 0.12
thyA 3074197 p.Pro92Arg missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3086846 c.32delA frameshift_variant 1.0
ald 3087019 p.Asp67Gly missense_variant 0.21
ald 3087458 c.639C>T synonymous_variant 0.23
ald 3087666 p.Tyr283Asn missense_variant 0.25
Rv3083 3448706 c.204dupG frameshift_variant 0.5
Rv3083 3448709 p.Trp69* stop_gained 0.5
Rv3083 3448712 c.210_213delCGAC frameshift_variant 0.5
Rv3083 3448721 p.Lys73Met missense_variant 0.5
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiB 3640879 c.-656C>T upstream_gene_variant 1.0
fbiA 3640901 p.Gln120Leu missense_variant 0.12
fbiB 3642421 p.Arg296Gln missense_variant 0.2
fbiB 3642590 c.1056G>T synonymous_variant 0.32
alr 3841362 p.Thr20Met missense_variant 0.88
rpoA 3878375 p.Ser45Ala missense_variant 0.5
rpoA 3878639 c.-132C>G upstream_gene_variant 0.13
clpC1 4038225 c.2479_2480insG frameshift_variant 0.2
clpC1 4039566 p.Val380Glu missense_variant 0.2
embC 4239966 p.Val35Ala missense_variant 0.11
embC 4240515 p.Val218Gly missense_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244448 p.Ala406Ser missense_variant 1.0
embB 4247101 c.588G>C synonymous_variant 0.67
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269643 p.Leu64Gln missense_variant 0.28
ethA 4326474 p.Pro334Ala missense_variant 0.83
ethA 4326497 p.Arg326Pro missense_variant 0.15
ethA 4326532 c.942C>A synonymous_variant 0.23
ethR 4327822 p.Glu92Lys missense_variant 0.12
ethA 4328022 c.-549G>A upstream_gene_variant 0.22
ethA 4328025 c.-552T>A upstream_gene_variant 0.22
ethA 4328227 c.-754C>A upstream_gene_variant 0.47
ethA 4328368 c.-895G>C upstream_gene_variant 0.11
whiB6 4338234 c.288A>G synonymous_variant 0.17
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408158 c.45G>C synonymous_variant 0.23