TB-Profiler result

Run: SRR11972438
Summary

Run ID: SRR11972438

Sample name:

Date: 03-04-2023 05:42:25

Number of reads: 534071

Percentage reads mapped: 71.63

Strain: lineage1.1.1

Drug-resistance: HR-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
lineage1 Indo-Oceanic EAI RD239 0.92
lineage1.1 Indo-Oceanic EAI3;EAI4;EAI5;EAI6 RD239 0.95
lineage1.1.1 Indo-Oceanic EAI4;EAI5 RD239 0.93
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
katG 2155168 p.Ser315Thr missense_variant 0.27 isoniazid
pncA 2289095 p.Asp49Glu missense_variant 0.33 pyrazinamide
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 6112 p.Met291Ile missense_variant 0.9
gyrA 6853 c.-449A>G upstream_gene_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8452 p.Ala384Val missense_variant 1.0
gyrA 9143 c.1842T>C synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
ccsA 620748 c.858T>G synonymous_variant 0.45
rpoB 760386 p.His194Tyr missense_variant 1.0
rpoB 760796 c.990A>G synonymous_variant 0.15
rpoB 761152 p.Leu449Gln missense_variant 0.22
rpoB 762144 p.Glu780Lys missense_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763884 p.Ala172Val missense_variant 0.73
rpoC 763886 c.517C>A synonymous_variant 0.73
rpoC 764326 c.957G>C synonymous_variant 0.18
rpoC 764341 c.972G>T synonymous_variant 0.2
rpoC 764359 c.990C>A synonymous_variant 0.13
rpoC 764368 c.999C>A synonymous_variant 0.12
rpoC 764371 c.1002G>C synonymous_variant 0.12
rpoC 764383 c.1014C>G synonymous_variant 0.12
rpoC 764387 c.1018T>C synonymous_variant 0.13
rpoC 764395 c.1026C>T synonymous_variant 0.14
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.14
rpoC 764410 c.1041G>T synonymous_variant 0.15
rpoC 764413 c.1044C>T synonymous_variant 0.18
rpoC 764419 c.1050C>G synonymous_variant 0.22
rpoC 765121 c.1752G>A synonymous_variant 0.18
rpoC 765171 p.Pro601Leu missense_variant 0.75
rpoC 765383 p.Met672Val missense_variant 0.82
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 778116 p.His122Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303819 p.Ala297Thr missense_variant 0.14
embR 1417019 p.Cys110Tyr missense_variant 0.88
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.12
rrs 1472151 n.306C>T non_coding_transcript_exon_variant 0.12
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.15
rrs 1472400 n.555C>T non_coding_transcript_exon_variant 0.15
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.13
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.14
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.16
rrs 1472953 n.1108_1109insA non_coding_transcript_exon_variant 0.2
rrs 1472975 n.1130T>A non_coding_transcript_exon_variant 0.19
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.16
rrs 1472986 n.1142delG non_coding_transcript_exon_variant 0.16
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.15
rrs 1472992 n.1147_1148insT non_coding_transcript_exon_variant 0.15
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.15
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.16
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.15
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.15
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.23
rrs 1473053 n.1208T>A non_coding_transcript_exon_variant 0.18
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.21
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.21
rrs 1473068 n.1223A>G non_coding_transcript_exon_variant 0.19
rrs 1473070 n.1225G>A non_coding_transcript_exon_variant 0.17
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.19
rrs 1473226 n.1381C>T non_coding_transcript_exon_variant 0.12
rrl 1474199 n.542G>A non_coding_transcript_exon_variant 0.12
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.12
rrl 1474202 n.545T>C non_coding_transcript_exon_variant 0.12
rrl 1474218 n.561T>A non_coding_transcript_exon_variant 0.12
rrl 1474228 n.571T>C non_coding_transcript_exon_variant 0.11
rrl 1474709 n.1052G>T non_coding_transcript_exon_variant 1.0
rrl 1474782 n.1125G>A non_coding_transcript_exon_variant 0.17
rrl 1474790 n.1133C>T non_coding_transcript_exon_variant 0.27
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.2
rrl 1474798 n.1141C>T non_coding_transcript_exon_variant 0.24
rrl 1474804 n.1147C>T non_coding_transcript_exon_variant 0.31
rrl 1474806 n.1149A>C non_coding_transcript_exon_variant 0.24
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.48
rrl 1474827 n.1170C>T non_coding_transcript_exon_variant 0.55
rrl 1474830 n.1173A>C non_coding_transcript_exon_variant 0.2
rrl 1474831 n.1174A>C non_coding_transcript_exon_variant 0.55
rrl 1474844 n.1187G>T non_coding_transcript_exon_variant 0.46
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.33
rrl 1474866 n.1209C>A non_coding_transcript_exon_variant 0.52
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.33
rrl 1474902 n.1245T>C non_coding_transcript_exon_variant 0.36
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.31
rrl 1474913 n.1256T>A non_coding_transcript_exon_variant 0.25
rrl 1474920 n.1263G>A non_coding_transcript_exon_variant 0.23
rrl 1475574 n.1917C>A non_coding_transcript_exon_variant 0.19
rrl 1475696 n.2039T>C non_coding_transcript_exon_variant 0.12
rrl 1475703 n.2046A>G non_coding_transcript_exon_variant 0.12
rrl 1475707 n.2050T>A non_coding_transcript_exon_variant 0.17
rrl 1475716 n.2059A>G non_coding_transcript_exon_variant 0.14
rrl 1475751 n.2094C>G non_coding_transcript_exon_variant 0.16
rrl 1475752 n.2095C>G non_coding_transcript_exon_variant 0.15
rrl 1475753 n.2096C>G non_coding_transcript_exon_variant 0.17
rrl 1475756 n.2100_2101insGGGGAA non_coding_transcript_exon_variant 0.17
rrl 1475761 n.2106_2113delCAAGGGTG non_coding_transcript_exon_variant 0.17
rrl 1475775 n.2118G>T non_coding_transcript_exon_variant 0.14
rrl 1475776 n.2119G>C non_coding_transcript_exon_variant 0.14
rrl 1475777 n.2120A>T non_coding_transcript_exon_variant 0.18
rrl 1475783 n.2126T>G non_coding_transcript_exon_variant 0.14
rrl 1475803 n.2146T>C non_coding_transcript_exon_variant 0.21
rrl 1475804 n.2147G>C non_coding_transcript_exon_variant 0.21
rrl 1475816 n.2159C>G non_coding_transcript_exon_variant 0.3
rrl 1475817 n.2160A>G non_coding_transcript_exon_variant 0.3
rrl 1475843 n.2186G>A non_coding_transcript_exon_variant 0.2
rrl 1475849 n.2192G>A non_coding_transcript_exon_variant 0.19
rrl 1475853 n.2196C>T non_coding_transcript_exon_variant 0.19
rrl 1475858 n.2201T>C non_coding_transcript_exon_variant 0.13
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.15
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.15
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.15
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.15
rrl 1476297 n.2640C>A non_coding_transcript_exon_variant 0.15
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.15
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.17
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.17
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.17
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.33
rrl 1476338 n.2681C>T non_coding_transcript_exon_variant 0.33
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.33
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.26
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.36
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.36
rrl 1476383 n.2726T>A non_coding_transcript_exon_variant 0.36
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.55
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.56
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.31
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.31
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.25
rrl 1476514 n.2857C>T non_coding_transcript_exon_variant 0.14
rrl 1476577 n.2920T>G non_coding_transcript_exon_variant 0.11
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.12
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.14
fabG1 1673357 c.-83G>A upstream_gene_variant 0.13
fabG1 1673359 c.-81T>C upstream_gene_variant 0.2
fabG1 1673361 c.-79C>G upstream_gene_variant 0.13
fabG1 1673380 c.-60C>G upstream_gene_variant 0.21
inhA 1674260 p.Ser20Leu missense_variant 0.12
inhA 1674958 c.759delC frameshift_variant 0.25
rpsA 1834319 p.Val260Ile missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154206 p.Ala636Thr missense_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2155553 p.Arg187Trp missense_variant 0.15
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2167983 p.Gly877Asp missense_variant 1.0
PPE35 2170048 p.Leu189Val missense_variant 0.14
PPE35 2170053 p.Thr187Ser missense_variant 0.14
PPE35 2170454 c.159C>G synonymous_variant 0.11
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518132 c.18C>T synonymous_variant 0.87
kasA 2518949 p.Ala279Ser missense_variant 0.14
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0
ahpC 2726070 c.-123G>A upstream_gene_variant 1.0
pepQ 2860580 c.-162G>T upstream_gene_variant 0.14
Rv2752c 3064632 c.1560C>T synonymous_variant 0.73
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448714 p.Asp71His missense_variant 0.85
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474597 c.591C>A synonymous_variant 0.88
fprA 3475159 p.Asn385Asp missense_variant 0.83
fprA 3475302 c.1296C>T synonymous_variant 0.92
fbiB 3642457 p.Arg308Leu missense_variant 0.15
alr 3841546 c.-126C>A upstream_gene_variant 0.14
rpoA 3878549 c.-42A>G upstream_gene_variant 0.75
rpoA 3878630 c.-124delC upstream_gene_variant 1.0
clpC1 4039508 c.1197G>C synonymous_variant 0.13
clpC1 4039526 c.1179G>C synonymous_variant 0.14
clpC1 4040517 p.Val63Ala missense_variant 1.0
embC 4239925 c.63C>T synonymous_variant 1.0
embC 4240671 p.Thr270Ile missense_variant 1.0
embC 4241042 p.Asn394Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243848 p.Val206Met missense_variant 1.0
embA 4244096 c.864C>T synonymous_variant 1.0
embA 4245969 p.Pro913Ser missense_variant 0.92
embB 4246514 c.1A>G start_lost 0.13
embB 4246544 p.Thr11Pro missense_variant 0.2
embB 4246548 p.Pro12Gln missense_variant 0.2
embB 4246556 p.Ala15Pro missense_variant 0.22
embB 4246563 p.Leu17Trp missense_variant 0.22
embB 4246567 c.54G>T synonymous_variant 0.2
embB 4247238 c.727delG frameshift_variant 0.13
embB 4247646 p.Glu378Ala missense_variant 1.0
embB 4249266 p.Pro918His missense_variant 0.17
ubiA 4269152 p.Ala228Ser missense_variant 0.94
ubiA 4269387 p.Glu149Asp missense_variant 0.94
aftB 4269606 c.-770T>C upstream_gene_variant 1.0
ethA 4327483 c.-10G>A upstream_gene_variant 0.89
ethA 4328055 c.-582A>G upstream_gene_variant 1.0
whiB6 4338242 p.Gln94Glu missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407873 c.330G>T synonymous_variant 0.91