TB-Profiler result

Run: SRR13423641
Summary

Run ID: SRR13423641

Sample name:

Date: 03-04-2023 08:54:56

Number of reads: 1678065

Percentage reads mapped: 47.71

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 1.0
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.99
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 761185 p.Glu460Gly missense_variant 0.11 rifampicin
katG 2155599 c.512delG frameshift_variant 0.17 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
gyrB 6144 p.His302Arg missense_variant 0.12
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 0.94
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576204 p.Ala286Val missense_variant 0.15
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 765943 p.Lys858Asn missense_variant 0.12
rpoC 766331 p.Leu988Met missense_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 775888 p.Gly865* stop_gained 0.12
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 1.0
mmpS5 778796 p.Ile37Asn missense_variant 0.11
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1302811 c.-120G>T upstream_gene_variant 0.14
Rv1258c 1406674 p.Arg223Trp missense_variant 0.11
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
embR 1417068 c.280T>C synonymous_variant 0.12
embR 1417250 p.Pro33His missense_variant 0.14
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472505 n.660G>A non_coding_transcript_exon_variant 0.23
rrs 1472507 n.662C>G non_coding_transcript_exon_variant 0.34
rrs 1472517 n.672T>A non_coding_transcript_exon_variant 0.43
rrs 1472518 n.673G>A non_coding_transcript_exon_variant 0.42
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.4
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.4
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.37
rrs 1472544 n.699C>T non_coding_transcript_exon_variant 0.37
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.38
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.4
rrs 1472570 n.725G>A non_coding_transcript_exon_variant 0.4
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.4
rrs 1472573 n.728C>T non_coding_transcript_exon_variant 0.39
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.37
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.38
rrs 1472591 n.746G>A non_coding_transcript_exon_variant 0.42
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.44
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.57
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.59
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.54
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.55
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.56
rrs 1472669 n.824_825insTAGA non_coding_transcript_exon_variant 0.62
rrs 1472678 n.833T>G non_coding_transcript_exon_variant 0.6
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.58
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.59
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.6
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.62
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.58
rrs 1472697 n.852T>C non_coding_transcript_exon_variant 0.59
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.59
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.59
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.59
rrl 1474738 n.1081G>A non_coding_transcript_exon_variant 0.15
rrl 1474740 n.1083G>T non_coding_transcript_exon_variant 0.21
rrl 1474747 n.1090C>A non_coding_transcript_exon_variant 0.4
rrl 1474753 n.1097delC non_coding_transcript_exon_variant 0.47
rrl 1474777 n.1120T>C non_coding_transcript_exon_variant 0.55
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.52
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.55
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.53
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.53
rrl 1474797 n.1140_1141insTATA non_coding_transcript_exon_variant 0.55
rrl 1474800 n.1144_1147delGTGC non_coding_transcript_exon_variant 0.54
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.55
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.57
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.56
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.57
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.57
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.64
rrl 1474852 n.1195T>C non_coding_transcript_exon_variant 0.66
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.74
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.74
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.43
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.13
rrl 1474905 n.1248T>C non_coding_transcript_exon_variant 0.14
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.14
rrl 1475463 n.1806A>G non_coding_transcript_exon_variant 0.12
rrl 1476135 n.2478T>C non_coding_transcript_exon_variant 0.33
rrl 1476141 n.2484A>G non_coding_transcript_exon_variant 0.7
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.73
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.67
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 0.67
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.69
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.67
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.68
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.67
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.67
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.67
rrl 1476210 n.2553G>T non_coding_transcript_exon_variant 0.67
rrl 1476211 n.2554G>T non_coding_transcript_exon_variant 0.67
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.67
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.67
rrl 1476215 n.2558C>A non_coding_transcript_exon_variant 0.72
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.85
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.92
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.92
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.91
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.88
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.88
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.87
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.87
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.86
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.85
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.85
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.86
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.86
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.86
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.92
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.92
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.93
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.92
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.91
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.91
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.86
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.85
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.85
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.88
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.86
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.8
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.74
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.7
rrl 1476523 n.2866T>C non_coding_transcript_exon_variant 0.69
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.69
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.69
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.69
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.73
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.73
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.71
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.7
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.7
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.69
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.7
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.67
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.6
rrl 1476595 n.2938C>T non_coding_transcript_exon_variant 0.14
inhA 1674210 c.9A>C synonymous_variant 1.0
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 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518307 p.Lys65Glu missense_variant 0.11
kasA 2518352 p.Met80Val missense_variant 0.11
kasA 2518361 p.Val83Ile missense_variant 0.12
kasA 2518600 c.490delG frameshift_variant 0.12
eis 2714663 c.667_669delTAC conservative_inframe_deletion 0.11
eis 2714898 c.435C>A synonymous_variant 0.12
folC 2746563 p.Pro346Ser missense_variant 0.14
folC 2746925 p.Asp225Gly missense_variant 0.94
ribD 2986988 c.150C>T synonymous_variant 0.15
ribD 2987589 p.Leu251Met missense_variant 0.15
ald 3086788 c.-32T>C upstream_gene_variant 1.0
ald 3087680 c.861G>A synonymous_variant 0.11
Rv3083 3448541 p.Gly13Asp missense_variant 0.14
Rv3083 3448622 p.Arg40His missense_variant 0.14
Rv3083 3449157 p.Phe218Leu missense_variant 0.17
Rv3083 3449892 c.1389C>A synonymous_variant 0.16
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474441 c.436delT frameshift_variant 0.18
fprA 3474444 c.438G>C synonymous_variant 0.18
fprA 3474449 p.Ala148Gly missense_variant 0.15
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640716 c.175_180delTGCCCG conservative_inframe_deletion 0.12
rpoA 3877599 c.909G>A synonymous_variant 0.12
clpC1 4040000 c.705C>T synonymous_variant 0.11
clpC1 4040287 p.Gln140* stop_gained 0.12
embC 4242059 p.Ala733Thr missense_variant 0.11
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243060 c.-173C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244417 p.Leu395Phe missense_variant 0.17
embA 4246260 p.Asp1010Tyr missense_variant 0.95
embB 4247323 c.810G>T synonymous_variant 0.12
embB 4248151 c.1638C>A synonymous_variant 0.13
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