TB-Profiler result

Run: SRR18002896
Summary

Run ID: SRR18002896

Sample name:

Date: 03-04-2023 19:08:45

Number of reads: 5452634

Percentage reads mapped: 97.1

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 1.0
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
gyrA 7582 p.Asp94Ala missense_variant 0.29 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1472733 n.888G>A non_coding_transcript_exon_variant 0.47 streptomycin
rrs 1473247 n.1402C>A non_coding_transcript_exon_variant 0.12 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247429 p.Met306Val missense_variant 1.0 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 7028 p.Ala597Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8164 p.Ala288Asp missense_variant 0.7
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576108 p.Ala254Gly missense_variant 0.33
ccsA 620625 p.Ile245Met missense_variant 1.0
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
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303882 p.Val318Ile missense_variant 1.0
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.12
rrs 1472122 n.277G>T non_coding_transcript_exon_variant 0.12
rrs 1472123 n.278A>T non_coding_transcript_exon_variant 0.12
rrs 1472124 n.279C>T non_coding_transcript_exon_variant 0.17
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.35
rrs 1472155 n.310C>T non_coding_transcript_exon_variant 0.13
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.23
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.24
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.18
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.11
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.11
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.27
rrs 1472234 n.389T>C non_coding_transcript_exon_variant 0.12
rrs 1472236 n.391C>G non_coding_transcript_exon_variant 0.12
rrs 1472240 n.395G>A non_coding_transcript_exon_variant 0.17
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.29
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.17
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.17
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.17
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.12
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.38
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.38
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.38
rrs 1472670 n.825G>T non_coding_transcript_exon_variant 0.37
rrs 1472673 n.828T>A non_coding_transcript_exon_variant 0.33
rrs 1472674 n.829T>C non_coding_transcript_exon_variant 0.2
rrs 1472675 n.830T>C non_coding_transcript_exon_variant 0.47
rrs 1472677 n.832C>T non_coding_transcript_exon_variant 0.44
rrs 1472681 n.837_838delTT non_coding_transcript_exon_variant 0.58
rrs 1472687 n.843dupT non_coding_transcript_exon_variant 0.4
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.47
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.53
rrs 1472701 n.856T>C non_coding_transcript_exon_variant 0.27
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.47
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.47
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.41
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.41
rrs 1472764 n.919G>A non_coding_transcript_exon_variant 0.12
rrs 1472767 n.922G>C non_coding_transcript_exon_variant 0.21
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.12
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.21
rrs 1472908 n.1063G>A non_coding_transcript_exon_variant 0.22
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.21
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.1
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.18
rrs 1473102 n.1257C>T non_coding_transcript_exon_variant 0.19
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.18
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.17
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.16
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.25
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.23
rrs 1473252 n.1407T>C non_coding_transcript_exon_variant 0.11
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.11
rrl 1474089 n.432C>T non_coding_transcript_exon_variant 0.22
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14
rrl 1474795 n.1138A>G non_coding_transcript_exon_variant 0.1
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.18
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.12
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.12
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.15
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.22
rrl 1475699 n.2042C>T non_coding_transcript_exon_variant 0.12
rrl 1475701 n.2044A>G non_coding_transcript_exon_variant 0.12
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.12
rrl 1475715 n.2058G>C non_coding_transcript_exon_variant 0.14
rrl 1475751 n.2094C>A non_coding_transcript_exon_variant 0.2
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.13
rrl 1475760 n.2103C>A non_coding_transcript_exon_variant 0.13
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.15
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.21
rrl 1475767 n.2110G>T non_coding_transcript_exon_variant 0.14
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.17
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.11
rrl 1475898 n.2241A>G non_coding_transcript_exon_variant 0.11
rrl 1475899 n.2242G>A non_coding_transcript_exon_variant 0.11
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.12
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.25
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.17
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.18
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.18
rrl 1476187 n.2530T>C non_coding_transcript_exon_variant 0.2
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.33
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.3
rrl 1476207 n.2550T>C non_coding_transcript_exon_variant 0.2
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.3
rrl 1476221 n.2564T>C non_coding_transcript_exon_variant 0.2
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.3
rrl 1476235 n.2578A>G non_coding_transcript_exon_variant 0.2
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.3
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.22
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.33
rrl 1476256 n.2599A>C non_coding_transcript_exon_variant 0.2
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.44
rrl 1476272 n.2615A>G non_coding_transcript_exon_variant 0.2
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.4
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.25
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.5
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.5
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.5
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.33
rrl 1476299 n.2642C>G non_coding_transcript_exon_variant 0.25
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.25
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.5
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.2
rrl 1476308 n.2651G>C non_coding_transcript_exon_variant 0.3
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.6
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.6
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.27
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.27
rrl 1476337 n.2680C>T non_coding_transcript_exon_variant 0.35
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.28
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.3
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.33
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.28
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.35
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.41
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.21
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.29
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.32
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.13
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.25
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.41
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.41
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.12
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.25
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.38
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.3
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.22
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.22
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.24
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.25
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.25
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.12
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834897 p.Ser452Arg missense_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
PPE35 2168548 p.Thr689Pro missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 0.99
embB 4247028 p.Leu172Arg missense_variant 0.25
aftB 4267647 p.Asp397Gly missense_variant 1.0
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
pncA 2289079 c.-1516_162del start_lost&conservative_inframe_deletion 1.0