TB-Profiler result

Run: ERR4832002
Summary

Run ID: ERR4832002

Sample name:

Date: 01-04-2023 21:15:53

Number of reads: 738572

Percentage reads mapped: 90.42

Strain: lineage2.1

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 0.98
lineage2.1 East-Asian (non-Beijing) None None 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
gyrA 7570 p.Ala90Val missense_variant 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.85 rifampicin
rpoC 764724 p.Phe452Ser missense_variant 0.76 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.91 isoniazid
pncA 2289204 p.Phe13Ser missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.97 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 5806 c.567C>A synonymous_variant 0.18
gyrB 6342 c.1106delG frameshift_variant 0.13
gyrB 6651 p.Arg471Leu missense_variant 0.2
gyrA 7078 c.-224A>G upstream_gene_variant 0.12
gyrA 7081 c.-221T>C upstream_gene_variant 0.12
gyrA 7084 c.-218A>G upstream_gene_variant 0.13
gyrA 7090 c.-212C>T upstream_gene_variant 0.12
gyrA 7093 c.-209T>C upstream_gene_variant 0.12
gyrA 7100 c.-202T>C upstream_gene_variant 0.13
gyrA 7123 c.-179C>G upstream_gene_variant 0.25
gyrA 7126 c.-176G>C upstream_gene_variant 0.25
gyrA 7129 c.-173T>G upstream_gene_variant 0.25
gyrA 7132 c.-170T>C upstream_gene_variant 0.25
gyrA 7135 c.-167G>A upstream_gene_variant 0.25
gyrA 7136 c.-166T>C upstream_gene_variant 0.25
gyrA 7141 c.-161T>G upstream_gene_variant 0.25
gyrA 7144 c.-158A>G upstream_gene_variant 0.25
gyrA 7153 c.-149G>C upstream_gene_variant 0.25
gyrA 7156 c.-146C>T upstream_gene_variant 0.25
gyrA 7168 c.-134C>G upstream_gene_variant 0.25
gyrA 7178 c.-124T>C upstream_gene_variant 0.25
gyrA 7186 c.-116C>G upstream_gene_variant 0.25
gyrA 7189 c.-113C>T upstream_gene_variant 0.25
gyrA 7198 c.-104C>T upstream_gene_variant 0.25
gyrB 7210 p.Asp657Glu missense_variant 0.2
gyrA 7213 c.-89G>A upstream_gene_variant 0.2
gyrA 7216 c.-86G>C upstream_gene_variant 0.2
gyrA 7225 c.-77T>C upstream_gene_variant 0.25
gyrA 7234 c.-68C>A upstream_gene_variant 0.25
gyrA 7286 c.-16T>C upstream_gene_variant 0.14
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7391 c.90C>T synonymous_variant 0.12
gyrA 7394 c.93T>C synonymous_variant 0.12
gyrA 7397 c.96G>C synonymous_variant 0.12
gyrA 7402 p.Ser34Asn missense_variant 0.12
gyrA 7412 c.111C>G synonymous_variant 0.12
gyrA 7421 c.120G>C synonymous_variant 0.12
gyrA 7424 c.123G>C synonymous_variant 0.12
gyrA 7427 c.126G>C synonymous_variant 0.12
gyrA 7433 c.132G>C synonymous_variant 0.12
gyrA 7442 c.141G>C synonymous_variant 0.1
gyrA 7475 c.174A>G synonymous_variant 0.11
gyrA 7480 p.Phe60Tyr missense_variant 0.19
gyrA 7484 c.183T>C synonymous_variant 0.19
gyrA 7499 c.198G>C synonymous_variant 0.21
gyrA 7516 p.Lys72Arg missense_variant 0.11
gyrA 7526 c.225G>C synonymous_variant 0.21
gyrA 7532 c.231T>G synonymous_variant 0.11
gyrA 7541 c.240C>G synonymous_variant 0.11
gyrA 7547 c.246C>T synonymous_variant 0.21
gyrA 7559 c.258G>C synonymous_variant 0.14
gyrA 7565 c.264C>T synonymous_variant 0.19
gyrA 7585 p.Ser95Thr missense_variant 0.95
gyrA 7613 c.312G>A synonymous_variant 0.15
gyrA 7622 c.321C>T synonymous_variant 0.17
gyrA 8378 p.Asp359Glu missense_variant 0.15
gyrA 8897 c.1596T>C synonymous_variant 0.12
gyrA 8903 c.1602T>C synonymous_variant 0.11
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491741 p.Phe320Tyr missense_variant 0.13
rpoB 760566 p.Ser254Pro missense_variant 0.7
rpoB 761027 c.1221A>C synonymous_variant 0.14
rpoB 761036 c.1230G>C synonymous_variant 0.13
rpoB 761037 c.1231T>C synonymous_variant 0.13
rpoB 761051 c.1245G>T synonymous_variant 0.13
rpoB 761054 c.1248G>C synonymous_variant 0.13
rpoB 761057 c.1251G>C synonymous_variant 0.13
rpoB 761060 c.1254C>G synonymous_variant 0.13
rpoB 761063 c.1257C>G synonymous_variant 0.13
rpoB 761084 c.1278C>A synonymous_variant 0.13
rpoC 762920 c.-450C>T upstream_gene_variant 0.13
rpoC 762929 c.-441G>C upstream_gene_variant 0.13
rpoC 762959 c.-411G>C upstream_gene_variant 0.12
rpoC 762995 c.-375G>T upstream_gene_variant 0.14
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763070 c.-300T>C upstream_gene_variant 0.1
rpoC 764752 c.1383G>C synonymous_variant 0.13
rpoC 764758 c.1389C>G synonymous_variant 0.17
rpoC 764764 c.1395T>C synonymous_variant 0.2
rpoC 764791 c.1422C>G synonymous_variant 0.18
rpoC 764803 c.1434C>T synonymous_variant 0.2
rpoC 764809 c.1440C>T synonymous_variant 0.18
rpoC 764810 p.Pro481Ala missense_variant 0.18
rpoC 764815 c.1446A>G synonymous_variant 0.17
rpoC 764824 c.1455T>C synonymous_variant 0.18
rpoC 764827 c.1458G>C synonymous_variant 0.31
rpoC 764858 c.1489T>C synonymous_variant 0.17
rpoC 764869 c.1500C>T synonymous_variant 0.17
rpoC 766448 p.Gly1027Cys missense_variant 0.14
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.95
mmpS5 778490 p.Val139Ala missense_variant 0.11
mmpS5 778748 p.Pro53His missense_variant 0.14
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304443 p.Ala505Thr missense_variant 1.0
embR 1416446 p.Tyr301Ser missense_variant 0.11
embR 1417264 c.84G>A synonymous_variant 0.22
atpE 1461033 c.-11delA upstream_gene_variant 0.17
atpE 1461114 p.Ala24Ser missense_variant 0.29
atpE 1461197 c.153A>C synonymous_variant 0.25
atpE 1461219 c.175T>C synonymous_variant 0.12
atpE 1461224 c.180T>G synonymous_variant 0.12
atpE 1461227 c.183G>A synonymous_variant 0.12
atpE 1461230 c.186G>C synonymous_variant 0.11
atpE 1461233 c.189A>G synonymous_variant 0.11
atpE 1461251 c.207G>C synonymous_variant 0.11
atpE 1461254 c.210T>C synonymous_variant 0.11
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.33
rrs 1472116 n.271C>A non_coding_transcript_exon_variant 0.17
rrs 1472380 n.535G>C non_coding_transcript_exon_variant 0.29
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.15
rrs 1472633 n.788C>A non_coding_transcript_exon_variant 0.25
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.17
rrs 1472846 n.1001C>A non_coding_transcript_exon_variant 0.2
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.2
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.2
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.2
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.18
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.18
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.18
rrs 1472861 n.1016G>T non_coding_transcript_exon_variant 0.18
rrl 1473594 n.-64A>G upstream_gene_variant 0.15
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.67
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.5
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.5
rrl 1474626 n.969T>C non_coding_transcript_exon_variant 0.5
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.4
rrl 1474636 n.979A>T non_coding_transcript_exon_variant 0.4
rrl 1474637 n.980C>T non_coding_transcript_exon_variant 0.4
rrl 1474638 n.981C>G non_coding_transcript_exon_variant 0.4
rrl 1474639 n.982G>T non_coding_transcript_exon_variant 0.4
rrl 1474640 n.983C>T non_coding_transcript_exon_variant 0.4
rrl 1475649 n.1992A>G non_coding_transcript_exon_variant 1.0
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 1.0
rrl 1475760 n.2105_2106delGC non_coding_transcript_exon_variant 0.29
rrl 1475764 n.2107A>T non_coding_transcript_exon_variant 0.29
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.29
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.4
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.4
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.8
rrl 1475989 n.2332T>C non_coding_transcript_exon_variant 0.4
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.4
rrl 1475993 n.2336C>T non_coding_transcript_exon_variant 0.4
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.4
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.4
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 1.0
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 1.0
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 1.0
rrl 1476034 n.2377C>G non_coding_transcript_exon_variant 1.0
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 1.0
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 1.0
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 1.0
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 1.0
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 1.0
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 1.0
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.5
rrl 1476058 n.2401T>C non_coding_transcript_exon_variant 0.5
rrl 1476085 n.2428G>A non_coding_transcript_exon_variant 1.0
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 1.0
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 1.0
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 1.0
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 1.0
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 1.0
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 1.0
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 1.0
rrl 1476114 n.2457T>C non_coding_transcript_exon_variant 1.0
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 1.0
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 1.0
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 1.0
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 1.0
rrl 1476165 n.2508T>A non_coding_transcript_exon_variant 1.0
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 1.0
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 1.0
rrl 1476204 n.2547C>T non_coding_transcript_exon_variant 1.0
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 1.0
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 1.0
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 1.0
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 1.0
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 1.0
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 1.0
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 1.0
rrl 1476267 n.2610G>T non_coding_transcript_exon_variant 1.0
rrl 1476276 n.2619C>A non_coding_transcript_exon_variant 1.0
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 1.0
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 1.0
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 1.0
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 1.0
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 1.0
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 1.0
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.5
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.5
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.5
inhA 1674300 c.99C>A synonymous_variant 1.0
inhA 1674427 p.Gly76Cys missense_variant 0.14
inhA 1674552 c.353delA frameshift_variant 0.15
rpsA 1834177 c.636A>C synonymous_variant 0.87
rpsA 1834303 c.762T>G synonymous_variant 0.11
rpsA 1834306 c.765T>C synonymous_variant 0.11
rpsA 1834348 c.807T>C synonymous_variant 0.11
rpsA 1834361 c.820T>C synonymous_variant 0.11
rpsA 1834366 c.825A>G synonymous_variant 0.11
rpsA 1834396 c.855G>C synonymous_variant 0.11
rpsA 1834411 c.870T>C synonymous_variant 0.1
rpsA 1834666 c.1125G>C synonymous_variant 0.11
rpsA 1834690 c.1149T>C synonymous_variant 0.12
rpsA 1834700 p.Gln387Ala missense_variant 0.14
rpsA 1834705 c.1164C>G synonymous_variant 0.14
rpsA 1834720 c.1179C>G synonymous_variant 0.13
rpsA 1834732 c.1191T>C synonymous_variant 0.13
rpsA 1834738 c.1197A>G synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154212 p.Leu634Ile missense_variant 0.16
katG 2154724 p.Arg463Leu missense_variant 1.0
katG 2156428 c.-317C>A upstream_gene_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168399 p.Glu738Asp missense_variant 0.13
PPE35 2168561 c.2052T>C synonymous_variant 0.22
PPE35 2168565 p.Pro683His missense_variant 0.22
PPE35 2168741 c.1872C>A synonymous_variant 0.13
PPE35 2169128 p.Asn495Lys missense_variant 0.12
PPE35 2169256 p.Phe453Ile missense_variant 0.17
PPE35 2169289 p.Phe442Leu missense_variant 0.13
PPE35 2169382 p.Trp411Arg missense_variant 0.15
PPE35 2169732 p.Asn294Thr missense_variant 0.96
PPE35 2170048 p.Leu189Val missense_variant 0.12
PPE35 2170053 p.Thr187Ser missense_variant 0.12
Rv1979c 2222406 c.759G>A synonymous_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289211 p.Asn11Asp missense_variant 0.11
Rv2752c 3064819 p.Gly458Val missense_variant 0.14
Rv2752c 3065518 p.Leu225Pro missense_variant 1.0
thyX 3067400 c.546C>T synonymous_variant 1.0
thyA 3074130 c.342G>C synonymous_variant 0.11
ald 3086700 c.-120G>T upstream_gene_variant 0.14
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448991 c.489delC frameshift_variant 0.18
Rv3083 3449001 c.498G>A synonymous_variant 0.17
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fbiA 3640357 c.-186G>A upstream_gene_variant 0.12
fbiB 3641262 c.-273C>A upstream_gene_variant 0.15
rpoA 3878143 p.Gly122Val missense_variant 0.14
clpC1 4038755 c.1950G>C synonymous_variant 0.11
clpC1 4038845 c.1860G>C synonymous_variant 0.1
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246088 c.-426A>G upstream_gene_variant 0.93
embB 4249314 c.2802delC frameshift_variant 0.15
embB 4249354 c.2841G>T synonymous_variant 0.18
aftB 4267087 p.Leu584Met missense_variant 0.18
aftB 4267647 p.Asp397Gly missense_variant 1.0
aftB 4267766 c.1071G>T synonymous_variant 0.15
aftB 4267827 p.Arg337Leu missense_variant 0.13
aftB 4268456 c.381G>A synonymous_variant 0.25
aftB 4268830 p.Arg3Trp missense_variant 0.13
aftB 4268858 c.-22G>T upstream_gene_variant 0.12
ethA 4326309 p.Ala389Ser missense_variant 0.22
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407926 c.276dupA frameshift_variant 1.0