TB-Profiler result

Run: SRR10869285
Summary

Run ID: SRR10869285

Sample name:

Date: 02-04-2023 19:47:10

Number of reads: 5948399

Percentage reads mapped: 94.78

Strain: lineage2.2.2

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.2 East-Asian (Beijing) Beijing-RD105/RD207 RD105;RD207 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 7572 p.Ser91Pro missense_variant 0.75 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.94 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.81 kanamycin, capreomycin, aminoglycosides, amikacin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.19 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289202 p.Cys14Arg missense_variant 0.99 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326333 p.Ala381Pro missense_variant 1.0 ethionamide
gid 4407967 p.Leu79Ser missense_variant 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7677 p.Ala126Ser missense_variant 0.15
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
rpoB 761084 c.1278C>G synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764560 c.1191T>C synonymous_variant 0.11
rpoC 764566 c.1197C>G synonymous_variant 0.11
rpoC 764817 p.Val483Gly missense_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.11
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.12
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.11
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.19
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.19
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.19
rrs 1472574 n.729T>A non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.18
rrs 1472584 n.739A>T non_coding_transcript_exon_variant 0.18
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.15
rrs 1472952 n.1107T>C non_coding_transcript_exon_variant 0.15
rrs 1472955 n.1110C>T non_coding_transcript_exon_variant 0.15
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.15
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.15
rrs 1472973 n.1128A>G non_coding_transcript_exon_variant 0.19
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.18
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.17
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.17
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.13
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.13
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.14
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.15
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.15
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.11
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.13
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.12
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.19
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.18
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.17
rrs 1473277 n.1432G>A non_coding_transcript_exon_variant 0.17
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.13
rrs 1473291 n.1446_1447insT non_coding_transcript_exon_variant 0.14
rrs 1473300 n.1455C>T non_coding_transcript_exon_variant 0.13
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.13
rrs 1473315 n.1470T>C non_coding_transcript_exon_variant 0.11
rrs 1473316 n.1471C>T non_coding_transcript_exon_variant 0.11
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.1
rrl 1474488 n.831G>T non_coding_transcript_exon_variant 0.17
rrl 1474496 n.839C>T non_coding_transcript_exon_variant 0.19
rrl 1474498 n.841G>T non_coding_transcript_exon_variant 0.19
rrl 1474505 n.848C>G non_coding_transcript_exon_variant 0.2
rrl 1474516 n.859C>A non_coding_transcript_exon_variant 0.21
rrl 1474529 n.872A>C non_coding_transcript_exon_variant 0.23
rrl 1474530 n.873G>A non_coding_transcript_exon_variant 0.23
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.23
rrl 1474539 n.882C>T non_coding_transcript_exon_variant 0.24
rrl 1474540 n.883T>G non_coding_transcript_exon_variant 0.23
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.11
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.1
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.11
rrl 1475722 n.2065G>T non_coding_transcript_exon_variant 0.13
rrl 1475869 n.2212C>A non_coding_transcript_exon_variant 0.2
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.23
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.22
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.18
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.18
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.14
rrl 1475937 n.2280A>T non_coding_transcript_exon_variant 0.16
rrl 1475943 n.2286G>A non_coding_transcript_exon_variant 0.15
rrl 1475952 n.2295A>G non_coding_transcript_exon_variant 0.14
rrl 1475963 n.2306G>T non_coding_transcript_exon_variant 0.11
rrl 1475970 n.2313C>T non_coding_transcript_exon_variant 0.11
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.16
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.22
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.23
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.23
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.2
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.2
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.12
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.21
rrl 1476429 n.2772A>T non_coding_transcript_exon_variant 0.21
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.12
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2221939 p.Arg409Gln missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3073806 c.666C>G synonymous_variant 0.28
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
clpC1 4038857 c.1848C>A synonymous_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
aftB 4267647 p.Asp397Gly missense_variant 1.0
ubiA 4269089 p.Ala249Thr missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.99
gid 4407927 p.Glu92Asp missense_variant 1.0