TB-Profiler result

Run: SRR11972407
Summary

Run ID: SRR11972407

Sample name:

Date: 03-04-2023 05:40:38

Number of reads: 859871

Percentage reads mapped: 88.94

Strain: lineage2.2.1

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
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 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol
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
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
mshA 575907 p.Ala187Val missense_variant 1.0
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 761998 p.Leu731Pro missense_variant 1.0
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 764058 p.Ala230Val missense_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
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472102 n.257G>A non_coding_transcript_exon_variant 0.12
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.12
rrs 1472112 n.267C>T non_coding_transcript_exon_variant 0.13
rrs 1472127 n.282C>T non_coding_transcript_exon_variant 0.12
rrs 1472129 n.284G>C non_coding_transcript_exon_variant 0.16
rrs 1472137 n.292G>A non_coding_transcript_exon_variant 0.23
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.31
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.31
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.29
rrs 1472203 n.358G>A non_coding_transcript_exon_variant 0.16
rrs 1472210 n.365A>C non_coding_transcript_exon_variant 0.16
rrs 1472213 n.368G>C non_coding_transcript_exon_variant 0.16
rrs 1472215 n.370A>G non_coding_transcript_exon_variant 0.16
rrs 1472222 n.377G>A non_coding_transcript_exon_variant 0.12
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.12
rrs 1472229 n.384C>T non_coding_transcript_exon_variant 0.12
rrs 1472518 n.673G>C non_coding_transcript_exon_variant 0.11
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.13
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.13
rrs 1472541 n.696T>G non_coding_transcript_exon_variant 0.12
rrs 1472544 n.699C>G non_coding_transcript_exon_variant 0.13
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.13
rrs 1472557 n.712G>A non_coding_transcript_exon_variant 0.22
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.22
rrs 1472579 n.734G>T non_coding_transcript_exon_variant 0.19
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.2
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.28
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.27
rrs 1472655 n.810G>A non_coding_transcript_exon_variant 0.37
rrs 1472658 n.813G>A non_coding_transcript_exon_variant 0.3
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.29
rrs 1472665 n.820G>A non_coding_transcript_exon_variant 0.3
rrs 1472678 n.833T>A non_coding_transcript_exon_variant 0.29
rrs 1472679 n.834T>C non_coding_transcript_exon_variant 0.29
rrs 1472682 n.839_843delGGGAT non_coding_transcript_exon_variant 0.29
rrs 1472689 n.844C>T non_coding_transcript_exon_variant 0.28
rrs 1472690 n.845C>A non_coding_transcript_exon_variant 0.29
rrs 1472695 n.850C>T non_coding_transcript_exon_variant 0.29
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.35
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.36
rrs 1472733 n.888G>C non_coding_transcript_exon_variant 0.4
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.39
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.34
rrs 1472742 n.897C>G non_coding_transcript_exon_variant 0.34
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.34
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.26
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.14
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.12
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.26
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.24
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.3
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.19
rrs 1473080 n.1235C>G non_coding_transcript_exon_variant 0.14
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.1
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.1
rrl 1474482 n.825G>T non_coding_transcript_exon_variant 0.14
rrl 1474494 n.837C>G non_coding_transcript_exon_variant 0.12
rrl 1474509 n.852G>C non_coding_transcript_exon_variant 0.11
rrl 1474527 n.870T>G non_coding_transcript_exon_variant 0.12
rrl 1474528 n.871T>C non_coding_transcript_exon_variant 0.12
rrl 1474530 n.873G>C non_coding_transcript_exon_variant 0.12
rrl 1474542 n.885A>C non_coding_transcript_exon_variant 0.11
rrl 1474552 n.895C>G non_coding_transcript_exon_variant 0.17
rrl 1474570 n.913G>T non_coding_transcript_exon_variant 0.16
rrl 1474578 n.921A>G non_coding_transcript_exon_variant 0.11
rrl 1474584 n.927C>G non_coding_transcript_exon_variant 0.11
rrl 1474779 n.1122G>A non_coding_transcript_exon_variant 0.2
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.2
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.17
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.17
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.17
rrl 1474801 n.1144G>A non_coding_transcript_exon_variant 0.18
rrl 1474802 n.1145T>C non_coding_transcript_exon_variant 0.18
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.18
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.22
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.32
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.33
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.33
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.36
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.38
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.44
rrl 1474869 n.1212G>T non_coding_transcript_exon_variant 0.44
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.52
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.45
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.41
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.38
rrl 1474920 n.1263G>C non_coding_transcript_exon_variant 0.34
rrl 1475122 n.1465C>T non_coding_transcript_exon_variant 0.16
rrl 1475129 n.1472G>T non_coding_transcript_exon_variant 0.18
rrl 1475144 n.1487G>C non_coding_transcript_exon_variant 0.19
rrl 1475154 n.1497C>A non_coding_transcript_exon_variant 0.19
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.13
rrl 1476153 n.2496T>C non_coding_transcript_exon_variant 0.19
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.17
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.17
rrl 1476165 n.2508T>C non_coding_transcript_exon_variant 0.17
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.12
rrl 1476195 n.2538C>A non_coding_transcript_exon_variant 0.12
rrl 1476196 n.2539C>A non_coding_transcript_exon_variant 0.12
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.12
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.12
rrl 1476204 n.2547C>A non_coding_transcript_exon_variant 0.12
rrl 1476212 n.2555T>C non_coding_transcript_exon_variant 0.12
rrl 1476225 n.2568T>G non_coding_transcript_exon_variant 0.38
rrl 1476229 n.2572C>G non_coding_transcript_exon_variant 0.43
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.57
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.57
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.6
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.57
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.57
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.57
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.56
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.56
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.56
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.58
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.58
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.58
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.67
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.71
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.74
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.72
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.67
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.67
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.65
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.6
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.6
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.61
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.69
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.7
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.67
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.66
rrl 1476519 n.2862C>G non_coding_transcript_exon_variant 0.67
rrl 1476524 n.2867C>A non_coding_transcript_exon_variant 0.66
rrl 1476525 n.2868A>G non_coding_transcript_exon_variant 0.65
rrl 1476530 n.2873C>T non_coding_transcript_exon_variant 0.65
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.64
rrl 1476537 n.2880A>G non_coding_transcript_exon_variant 0.64
rrl 1476538 n.2881A>G non_coding_transcript_exon_variant 0.64
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.65
rrl 1476547 n.2890C>T non_coding_transcript_exon_variant 0.67
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.71
rrl 1476573 n.2916A>C non_coding_transcript_exon_variant 0.69
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.69
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.66
rrl 1476596 n.2939C>T non_coding_transcript_exon_variant 0.13
rrl 1476608 n.2951C>A non_coding_transcript_exon_variant 0.35
rrl 1476614 n.2957A>G non_coding_transcript_exon_variant 0.32
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.16
rrl 1476630 n.2973A>G non_coding_transcript_exon_variant 0.1
rrl 1476637 n.2980C>G non_coding_transcript_exon_variant 0.1
fabG1 1673380 c.-60C>G upstream_gene_variant 0.23
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
katG 2155746 c.366C>A synonymous_variant 0.12
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.16
PPE35 2170053 p.Thr187Ser missense_variant 0.18
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747437 p.Met54Ile missense_variant 1.0
Rv2752c 3066094 p.Val33Ala missense_variant 0.12
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
fbiB 3641616 c.83_88delATCTGA disruptive_inframe_deletion 0.14
fbiB 3641626 p.Ala31Gly missense_variant 0.14
embC 4241958 p.Arg699Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4244862 c.1630C>T synonymous_variant 0.12
embB 4246641 p.Ala43Val missense_variant 0.15
aftB 4267647 p.Asp397Gly missense_variant 1.0
ethA 4327056 p.Tyr140Asp missense_variant 0.12
ethA 4327472 c.2T>G start_lost 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