TB-Profiler result

Run: ERR4829530
Summary

Run ID: ERR4829530

Sample name:

Date: 01-04-2023 19:32:14

Number of reads: 3221175

Percentage reads mapped: 81.45

Strain: lineage4.8

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
gyrA 7581 p.Asp94Tyr missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.91 rifampicin
rpoC 764363 p.Gly332Arg missense_variant 0.8 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.95 ethambutol
ethA 4326082 c.1391dupA frameshift_variant 1.0 ethionamide, ethionamide
gid 4407830 p.Gln125* stop_gained 1.0 streptomycin
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
rpoB 760184 c.378A>G synonymous_variant 0.12
rpoB 760196 c.390C>G synonymous_variant 0.14
rpoB 760235 c.429T>C synonymous_variant 0.16
rpoB 760244 c.438G>C synonymous_variant 0.17
rpoB 760283 c.477G>C synonymous_variant 0.19
rpoB 760298 c.492G>C synonymous_variant 0.19
rpoB 760310 c.504G>C synonymous_variant 0.17
rpoB 760316 c.510C>G synonymous_variant 0.17
rpoB 760331 c.525G>T synonymous_variant 0.15
rpoB 760334 c.528G>A synonymous_variant 0.15
rpoB 760340 c.534G>T synonymous_variant 0.15
rpoB 760357 p.Thr184Asn missense_variant 0.16
rpoB 760361 c.555T>C synonymous_variant 0.14
rpoB 760376 p.Asp190Glu missense_variant 0.16
rpoB 760406 c.600G>C synonymous_variant 0.16
rpoB 760407 p.Ser201Gly missense_variant 0.16
rpoB 760422 c.616_618delCTCinsTTG synonymous_variant 0.18
rpoB 760430 c.624T>C synonymous_variant 0.18
rpoB 760457 c.651C>T synonymous_variant 0.14
rpoB 760463 c.657C>T synonymous_variant 0.13
rpoB 762176 c.2370T>C synonymous_variant 0.12
rpoB 762218 c.2412T>C synonymous_variant 0.13
rpoB 762245 c.2439G>C synonymous_variant 0.13
rpoC 762989 c.-381G>A upstream_gene_variant 0.14
rpoC 762995 c.-375G>T upstream_gene_variant 0.14
rpoC 763007 c.-363C>T upstream_gene_variant 0.13
rpoC 763031 c.-339T>C upstream_gene_variant 0.12
rpoC 763053 c.-317T>C upstream_gene_variant 0.13
rpoC 763070 c.-300T>C upstream_gene_variant 0.13
rpoC 763528 c.159G>A synonymous_variant 0.13
rpoC 763531 c.162G>T synonymous_variant 0.13
rpoC 763546 c.177A>G synonymous_variant 0.13
rpoC 763570 c.201G>C synonymous_variant 0.16
rpoC 763573 c.204G>C synonymous_variant 0.15
rpoC 763594 c.225C>T synonymous_variant 0.15
rpoC 763621 c.252C>T synonymous_variant 0.16
rpoC 763699 c.330G>T synonymous_variant 0.12
rpoC 763705 c.336G>C synonymous_variant 0.12
rpoC 764344 c.975C>T synonymous_variant 0.14
rpoC 764353 c.984G>T synonymous_variant 0.17
rpoC 764371 c.1002G>T synonymous_variant 0.2
rpoC 764380 c.1011G>C synonymous_variant 0.17
rpoC 764387 c.1018T>C synonymous_variant 0.16
rpoC 764405 c.1036_1038delAGGinsCGC synonymous_variant 0.14
rpoC 764485 c.1116G>C synonymous_variant 0.15
rpoC 764491 c.1122G>T synonymous_variant 0.16
rpoC 764497 c.1128A>G synonymous_variant 0.15
rpoC 764500 c.1131C>G synonymous_variant 0.14
rpoC 764575 c.1206T>G synonymous_variant 0.15
rpoC 764605 c.1236G>C synonymous_variant 0.15
rpoC 764611 c.1242G>T synonymous_variant 0.15
rpoC 764621 c.1252_1254delCTCinsTTG synonymous_variant 0.15
rpoC 764626 c.1257C>T synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.15
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 764668 c.1299C>T synonymous_variant 0.13
rpoC 764713 c.1344G>C synonymous_variant 0.16
rpoC 764719 c.1350G>A synonymous_variant 0.17
rpoC 764746 c.1377G>T synonymous_variant 0.17
rpoC 764752 c.1383G>C synonymous_variant 0.16
rpoC 764758 c.1389C>G synonymous_variant 0.16
rpoC 764764 c.1395T>C synonymous_variant 0.15
rpoC 764791 c.1422C>G synonymous_variant 0.16
rpoC 764803 c.1434C>T synonymous_variant 0.19
rpoC 764809 c.1440C>T synonymous_variant 0.18
rpoC 764815 c.1446A>G synonymous_variant 0.19
rpoC 764827 c.1458G>C synonymous_variant 0.19
rpoC 764858 c.1489T>C synonymous_variant 0.21
rpoC 764869 c.1500C>T synonymous_variant 0.21
rpoC 764875 c.1506C>T synonymous_variant 0.2
rpoC 764878 c.1509C>G synonymous_variant 0.19
rpoC 764887 c.1518G>C synonymous_variant 0.18
rpoC 764888 c.1519T>C synonymous_variant 0.18
rpoC 764911 c.1542A>G synonymous_variant 0.16
rpoC 764912 p.Met515Gln missense_variant 0.16
rpoC 764935 c.1566T>C synonymous_variant 0.15
rpoC 764948 c.1579T>C synonymous_variant 0.13
rpoC 764968 c.1599T>C synonymous_variant 0.14
rpoC 765008 p.Leu547Val missense_variant 1.0
rpoC 766085 p.Pro906Ala missense_variant 1.0
rpoC 766909 c.3540G>C synonymous_variant 0.14
rpoC 766911 p.Ile1181Thr missense_variant 0.14
rpoC 766915 p.Asp1182Glu missense_variant 0.15
rpoC 766921 c.3552G>C synonymous_variant 0.16
rpoC 766931 p.Ala1188Thr missense_variant 0.17
rpoC 766942 c.3573C>T synonymous_variant 0.19
rpoC 766945 c.3576A>C synonymous_variant 0.19
rpoC 766948 c.3579G>C synonymous_variant 0.19
rpoC 766960 c.3591C>T synonymous_variant 0.18
rpoC 766963 c.3594T>C synonymous_variant 0.18
rpoC 766978 c.3609C>T synonymous_variant 0.19
rpoC 766981 c.3612T>C synonymous_variant 0.19
rpoC 766996 c.3627C>T synonymous_variant 0.18
rpoC 767002 c.3633G>C synonymous_variant 0.18
rpoC 767008 c.3639G>A synonymous_variant 0.2
rpoC 767020 c.3651C>G synonymous_variant 0.18
rpoC 767023 c.3654C>T synonymous_variant 0.17
rpoC 767059 c.3690T>G synonymous_variant 0.13
rpoC 767098 c.3729T>C synonymous_variant 0.13
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779062 p.Gly25Cys missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1471922 n.78delT non_coding_transcript_exon_variant 0.14
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.15
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.17
rrs 1472042 n.197T>G non_coding_transcript_exon_variant 0.12
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.14
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.14
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.18
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.2
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.2
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.2
rrs 1472446 n.601T>A non_coding_transcript_exon_variant 0.15
rrs 1472452 n.607G>A non_coding_transcript_exon_variant 0.15
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.12
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.19
rrs 1472847 n.1002G>C non_coding_transcript_exon_variant 0.13
rrs 1472849 n.1004C>G non_coding_transcript_exon_variant 0.13
rrs 1472850 n.1005T>C non_coding_transcript_exon_variant 0.13
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.14
rrs 1472858 n.1013G>T non_coding_transcript_exon_variant 0.14
rrs 1472859 n.1014G>C non_coding_transcript_exon_variant 0.14
rrs 1472860 n.1015C>G non_coding_transcript_exon_variant 0.14
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.3
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.26
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.26
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.16
rrl 1473833 n.176G>A non_coding_transcript_exon_variant 0.15
rrl 1473836 n.179A>G non_coding_transcript_exon_variant 0.18
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.15
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.16
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.16
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.14
rrl 1473899 n.242A>G non_coding_transcript_exon_variant 0.14
rrl 1473916 n.259C>A non_coding_transcript_exon_variant 0.14
rrl 1473922 n.265A>G non_coding_transcript_exon_variant 0.19
rrl 1473923 n.266C>G non_coding_transcript_exon_variant 0.14
rrl 1473924 n.267_268insT non_coding_transcript_exon_variant 0.14
rrl 1473935 n.278C>T non_coding_transcript_exon_variant 0.16
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.16
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.15
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.15
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.15
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.11
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.12
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.15
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.13
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.15
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.15
rrl 1475764 n.2107A>C non_coding_transcript_exon_variant 0.15
rrl 1475765 n.2108A>G non_coding_transcript_exon_variant 0.15
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.31
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.33
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.33
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.22
rrl 1476045 n.2388G>T non_coding_transcript_exon_variant 0.22
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.22
rrl 1476056 n.2399G>A non_coding_transcript_exon_variant 0.22
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.28
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.24
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.2
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.2
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.21
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.21
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.22
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.26
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.2
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.2
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.21
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.22
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.18
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.22
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.22
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.17
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.19
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.2
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.25
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.22
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.2
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.18
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.17
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.18
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.19
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.18
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.16
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.16
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.17
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.15
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.15
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.15
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.15
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.15
rpsA 1833664 c.123C>G synonymous_variant 0.13
rpsA 1833676 c.135A>G synonymous_variant 0.13
rpsA 1833694 c.153G>T synonymous_variant 0.12
rpsA 1833979 c.438T>C synonymous_variant 0.12
rpsA 1833991 c.450C>A synonymous_variant 0.12
rpsA 1834345 c.804C>T synonymous_variant 0.12
rpsA 1834348 c.807T>C synonymous_variant 0.13
rpsA 1834361 c.820T>C synonymous_variant 0.14
rpsA 1834366 c.825A>G synonymous_variant 0.13
rpsA 1834387 c.846C>T synonymous_variant 0.14
rpsA 1834396 c.855G>C synonymous_variant 0.14
rpsA 1834408 c.867C>T synonymous_variant 0.12
tlyA 1917972 c.33A>G synonymous_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv3083 3448497 c.-7T>A upstream_gene_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
rpoA 3878143 p.Gly122Asp missense_variant 0.13
rpoA 3878145 c.363C>G synonymous_variant 0.14
rpoA 3878160 c.348C>G synonymous_variant 0.12
rpoA 3878169 c.339G>C synonymous_variant 0.13
rpoA 3878175 c.333G>C synonymous_variant 0.14
rpoA 3878184 c.324C>T synonymous_variant 0.14
rpoA 3878193 c.315T>C synonymous_variant 0.12
rpoA 3878196 p.Glu104Ala missense_variant 0.12
rpoA 3878205 c.303T>C synonymous_variant 0.13
rpoA 3878217 c.291A>G synonymous_variant 0.16
rpoA 3878247 c.261G>C synonymous_variant 0.14
rpoA 3878256 c.252G>C synonymous_variant 0.15
rpoA 3878264 p.Ser82Gly missense_variant 0.14
rpoA 3878271 c.237T>C synonymous_variant 0.14
rpoA 3878283 p.Glu75Asp missense_variant 0.13
clpC1 4038812 c.1893T>C synonymous_variant 0.14
clpC1 4038815 c.1890G>A synonymous_variant 0.14
clpC1 4038878 c.1827A>G synonymous_variant 0.19
clpC1 4038890 c.1815G>A synonymous_variant 0.2
clpC1 4038905 c.1800A>C synonymous_variant 0.17
clpC1 4038908 c.1797C>G synonymous_variant 0.17
clpC1 4038911 c.1794G>T synonymous_variant 0.17
clpC1 4038914 c.1791G>C synonymous_variant 0.17
clpC1 4038917 c.1788C>T synonymous_variant 0.17
clpC1 4038923 c.1782A>G synonymous_variant 0.17
clpC1 4038941 c.1764G>C synonymous_variant 0.15
clpC1 4038953 c.1752A>G synonymous_variant 0.15
clpC1 4038956 c.1749T>C synonymous_variant 0.15
clpC1 4038965 c.1740T>C synonymous_variant 0.14
clpC1 4038980 c.1725C>T synonymous_variant 0.14
clpC1 4038989 c.1716T>C synonymous_variant 0.15
clpC1 4038997 c.1708T>C synonymous_variant 0.14
clpC1 4039064 c.1641C>T synonymous_variant 0.14
clpC1 4039067 c.1638G>C synonymous_variant 0.13
clpC1 4039085 c.1620A>G synonymous_variant 0.16
clpC1 4039090 c.1615C>T synonymous_variant 0.16
clpC1 4039097 c.1608G>C synonymous_variant 0.16
clpC1 4039100 c.1605C>T synonymous_variant 0.17
clpC1 4039106 c.1599G>T synonymous_variant 0.18
clpC1 4039112 c.1593C>G synonymous_variant 0.19
clpC1 4039118 c.1587C>G synonymous_variant 0.18
clpC1 4039121 c.1584T>C synonymous_variant 0.18
clpC1 4039142 c.1563A>G synonymous_variant 0.17
clpC1 4039145 c.1560G>C synonymous_variant 0.17
clpC1 4039169 p.Glu512Asp missense_variant 0.2
clpC1 4039172 c.1533A>G synonymous_variant 0.21
clpC1 4039178 c.1527G>C synonymous_variant 0.19
clpC1 4039183 c.1522T>C synonymous_variant 0.19
clpC1 4039187 c.1518G>C synonymous_variant 0.18
clpC1 4039190 c.1515C>G synonymous_variant 0.19
clpC1 4039208 c.1497C>G synonymous_variant 0.13
clpC1 4039622 c.1083C>T synonymous_variant 0.13
clpC1 4039649 c.1056G>C synonymous_variant 0.16
clpC1 4039664 c.1041G>C synonymous_variant 0.17
clpC1 4039670 c.1035G>C synonymous_variant 0.19
clpC1 4039682 c.1023C>G synonymous_variant 0.19
clpC1 4039694 c.1011G>C synonymous_variant 0.2
clpC1 4039724 c.981A>G synonymous_variant 0.23
clpC1 4039733 c.972G>C synonymous_variant 0.22
clpC1 4039742 c.963C>T synonymous_variant 0.2
clpC1 4039748 c.957G>C synonymous_variant 0.19
clpC1 4039751 c.954A>G synonymous_variant 0.2
clpC1 4039757 c.948A>G synonymous_variant 0.21
clpC1 4039763 c.942C>G synonymous_variant 0.21
clpC1 4039766 c.939T>C synonymous_variant 0.22
clpC1 4039769 c.936C>G synonymous_variant 0.22
clpC1 4039778 c.927A>G synonymous_variant 0.21
clpC1 4039787 c.916_918delTCGinsAGC synonymous_variant 0.21
clpC1 4039823 c.882T>A synonymous_variant 0.22
clpC1 4039829 c.874_876delTTGinsCTC synonymous_variant 0.21
clpC1 4039850 c.855T>C synonymous_variant 0.22
clpC1 4039865 c.840T>C synonymous_variant 0.21
clpC1 4039904 c.801A>G synonymous_variant 0.21
clpC1 4039913 c.792C>T synonymous_variant 0.2
clpC1 4039931 c.774T>C synonymous_variant 0.17
clpC1 4039934 c.771G>A synonymous_variant 0.16
clpC1 4039937 c.768G>C synonymous_variant 0.16
clpC1 4039946 c.759A>T synonymous_variant 0.15
clpC1 4039952 c.753T>C synonymous_variant 0.13
clpC1 4040411 c.294T>C synonymous_variant 0.14
clpC1 4040423 c.282A>G synonymous_variant 0.15
clpC1 4040431 c.274T>C synonymous_variant 0.14
clpC1 4040433 c.271_272delAGinsTC synonymous_variant 0.14
clpC1 4040450 c.255A>G synonymous_variant 0.13
clpC1 4040456 c.249C>T synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0