TB-Profiler result

Run: SRR6824572
Summary

Run ID: SRR6824572

Sample name:

Date: 04-04-2023 16:47:19

Number of reads: 2669112

Percentage reads mapped: 83.13

Strain: lineage2.2.1

Drug-resistance: MDR-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 1.0
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
rpoB 761139 p.His445Asn missense_variant 0.97 rifampicin
rpoB 761154 p.Ser450Ala missense_variant 0.5 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 0.98
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
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
Rv1258c 1406760 c.580_581insC frameshift_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 0.1
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.16
rrs 1472953 n.1111_1112delTC non_coding_transcript_exon_variant 0.26
rrs 1472959 n.1114_1115insTA non_coding_transcript_exon_variant 0.26
rrs 1472969 n.1125delC non_coding_transcript_exon_variant 0.26
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.26
rrs 1472974 n.1129A>C non_coding_transcript_exon_variant 0.26
rrs 1472975 n.1130T>G non_coding_transcript_exon_variant 0.26
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.27
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.27
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.28
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.29
rrs 1472990 n.1145A>T non_coding_transcript_exon_variant 0.29
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.28
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.28
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.23
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.13
rrl 1475866 n.2209T>A non_coding_transcript_exon_variant 0.12
rrl 1475876 n.2220_2221delCT non_coding_transcript_exon_variant 0.12
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.11
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.16
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.16
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.16
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.15
rrl 1476196 n.2539C>G non_coding_transcript_exon_variant 0.15
rrl 1476197 n.2540T>C non_coding_transcript_exon_variant 0.16
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.16
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.16
rrl 1476209 n.2552A>G non_coding_transcript_exon_variant 0.16
rrl 1476210 n.2553G>C non_coding_transcript_exon_variant 0.16
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.16
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.16
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.16
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.16
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.16
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.3
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.29
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.3
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.34
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.3
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.29
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.3
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.3
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.3
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.4
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.4
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.41
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.52
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.51
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.5
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.49
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.49
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.48
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.42
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.42
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.42
rrl 1476411 n.2754G>T non_coding_transcript_exon_variant 0.41
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.36
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36
rrl 1476463 n.2806C>A non_coding_transcript_exon_variant 0.31
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.3
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.24
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.17
rrl 1476515 n.2858C>T non_coding_transcript_exon_variant 0.13
rrl 1476517 n.2860C>T non_coding_transcript_exon_variant 0.14
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.14
rrl 1476524 n.2867C>T non_coding_transcript_exon_variant 0.14
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.14
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.14
rrl 1476536 n.2879G>T non_coding_transcript_exon_variant 0.14
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.14
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.14
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.14
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.15
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.17
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.16
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.16
rpsA 1834177 c.636A>C synonymous_variant 0.98
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 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066194 c.-3G>T upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449504 p.Gly334Ala missense_variant 0.93
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
rpoA 3878620 c.-113C>T upstream_gene_variant 0.2
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
ethA 4326676 p.Ser266Arg missense_variant 1.0
whiB6 4338537 c.-16T>C upstream_gene_variant 0.97
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