TB-Profiler result

Run: ERR4818811

Summary

Run ID: ERR4818811

Sample name:

Date: 17-08-2022 08:25:55

Number of reads: 1216841

Percentage reads mapped: 82.72

Strain: lineage2.2.1

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 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
gyrA 7582 p.Asp94Ala missense_variant 0.96 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.89 rifampicin
rpoC 764841 p.Ile491Thr missense_variant 0.87 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288764 p.Thr160Pro missense_variant 1.0 pyrazinamide
ethA 4326317 c.1156delT frameshift_variant 1.0 ethionamide
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 8354 c.1053G>C synonymous_variant 0.1
gyrA 8840 c.1539C>T synonymous_variant 0.15
gyrA 8852 c.1551T>C synonymous_variant 0.17
gyrA 8858 c.1557T>C synonymous_variant 0.17
gyrA 8870 c.1569G>C synonymous_variant 0.14
gyrA 8897 c.1596T>C synonymous_variant 0.14
gyrA 8915 c.1614A>G synonymous_variant 0.23
gyrA 8924 c.1623C>T synonymous_variant 0.25
gyrA 8939 c.1638T>G synonymous_variant 0.21
gyrA 8945 c.1644G>C synonymous_variant 0.18
gyrA 8946 c.1645_1647delTTGinsCTC synonymous_variant 0.19
gyrA 8967 p.Ala556Lys missense_variant 0.21
gyrA 8990 c.1689C>G synonymous_variant 0.23
gyrA 8993 c.1692C>T synonymous_variant 0.22
gyrA 8996 c.1695T>C synonymous_variant 0.22
gyrA 8998 p.Leu566Trp missense_variant 0.22
gyrA 9044 c.1743C>G synonymous_variant 0.12
gyrA 9051 c.1750T>C synonymous_variant 0.13
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 760184 c.378A>G synonymous_variant 0.21
rpoB 760196 c.390C>G synonymous_variant 0.19
rpoB 760223 c.417T>C synonymous_variant 0.21
rpoB 760235 c.429T>C synonymous_variant 0.21
rpoB 760244 c.438G>C synonymous_variant 0.19
rpoB 760376 p.Asp190Glu missense_variant 0.14
rpoB 760382 c.576G>C synonymous_variant 0.14
rpoB 760400 c.594G>C synonymous_variant 0.19
rpoB 760406 c.600G>C synonymous_variant 0.19
rpoB 760407 p.Ser201Gly missense_variant 0.19
rpoB 760412 c.606C>T synonymous_variant 0.19
rpoB 760415 c.609C>T synonymous_variant 0.19
rpoB 760418 c.612G>A synonymous_variant 0.19
rpoB 760430 c.624T>C synonymous_variant 0.3
rpoB 760433 c.627C>T synonymous_variant 0.32
rpoB 760454 c.648C>G synonymous_variant 0.35
rpoB 760457 c.651C>T synonymous_variant 0.38
rpoB 760469 c.663C>T synonymous_variant 0.29
rpoB 760475 c.669A>G synonymous_variant 0.21
rpoB 760478 c.672C>T synonymous_variant 0.21
rpoB 760481 c.675G>T synonymous_variant 0.23
rpoB 760484 c.678A>G synonymous_variant 0.23
rpoB 760487 c.681G>C synonymous_variant 0.31
rpoB 760502 c.696C>G synonymous_variant 0.25
rpoB 760508 c.702G>A synonymous_variant 0.24
rpoB 760511 c.705G>C synonymous_variant 0.22
rpoB 760522 p.Ser239Asn missense_variant 0.17
rpoB 760532 c.726T>C synonymous_variant 0.26
rpoB 760541 c.735G>T synonymous_variant 0.21
rpoB 760561 c.757_758delCG frameshift_variant 0.24
rpoB 760571 c.765G>C synonymous_variant 0.24
rpoB 760588 p.Thr261Ile missense_variant 0.18
rpoB 760591 p.Val262Ala missense_variant 0.22
rpoB 760595 c.789C>T synonymous_variant 0.24
rpoB 760596 p.Thr264Pro missense_variant 0.25
rpoB 760607 c.801G>C synonymous_variant 0.31
rpoB 760611 c.805T>C synonymous_variant 0.26
rpoB 760634 c.828T>C synonymous_variant 0.12
rpoB 760646 c.840C>G synonymous_variant 0.12
rpoB 760655 c.849A>G synonymous_variant 0.12
rpoB 760661 c.855A>C synonymous_variant 0.12
rpoB 761015 c.1209G>C synonymous_variant 0.14
rpoB 761027 c.1221A>C synonymous_variant 0.14
rpoB 761036 c.1230G>C synonymous_variant 0.14
rpoB 761037 c.1231T>C synonymous_variant 0.13
rpoB 761165 c.1359G>C synonymous_variant 0.11
rpoB 761234 c.1428G>C synonymous_variant 0.14
rpoB 761249 c.1443A>G synonymous_variant 0.14
rpoB 761255 c.1449T>G synonymous_variant 0.14
rpoB 761258 c.1452G>A synonymous_variant 0.14
rpoB 761261 c.1455G>C synonymous_variant 0.15
rpoB 761264 c.1458C>G synonymous_variant 0.15
rpoB 761273 c.1467T>C synonymous_variant 0.18
rpoB 761282 c.1476C>T synonymous_variant 0.15
rpoB 761288 c.1482G>T synonymous_variant 0.15
rpoB 761645 c.1839C>G synonymous_variant 0.11
rpoB 761648 c.1842T>C synonymous_variant 0.11
rpoB 762038 c.2232C>T synonymous_variant 0.15
rpoB 762047 c.2241G>A synonymous_variant 0.15
rpoB 762053 c.2247T>C synonymous_variant 0.14
rpoB 762056 c.2250G>A synonymous_variant 0.14
rpoB 762065 c.2259T>G synonymous_variant 0.14
rpoB 762083 c.2277T>C synonymous_variant 0.12
rpoB 762101 c.2295C>G synonymous_variant 0.11
rpoB 762114 p.Ile770Val missense_variant 0.11
rpoB 762194 c.2388G>C synonymous_variant 0.12
rpoB 762221 c.2415G>A synonymous_variant 0.22
rpoB 762233 c.2427G>C synonymous_variant 0.28
rpoB 762236 c.2430G>C synonymous_variant 0.24
rpoB 762245 c.2439G>C synonymous_variant 0.27
rpoB 762284 c.2478G>T synonymous_variant 0.26
rpoB 762293 c.2487T>C synonymous_variant 0.18
rpoB 762296 c.2490G>C synonymous_variant 0.17
rpoB 762317 c.2511A>G synonymous_variant 0.11
rpoB 762329 c.2523G>C synonymous_variant 0.11
rpoC 763031 c.-339T>C upstream_gene_variant 1.0
rpoC 763040 c.-330C>G upstream_gene_variant 0.13
rpoC 763070 c.-300T>C upstream_gene_variant 0.13
rpoC 763082 c.-288C>T upstream_gene_variant 0.13
rpoC 763115 c.-255T>C upstream_gene_variant 0.14
rpoC 763127 c.-243G>C upstream_gene_variant 0.11
rpoC 763570 c.201G>C synonymous_variant 0.17
rpoC 763594 c.225C>T synonymous_variant 0.14
rpoC 763618 c.249C>T synonymous_variant 0.14
rpoC 763741 c.372C>T synonymous_variant 0.14
rpoC 763747 c.378G>A synonymous_variant 0.15
rpoC 763765 c.396T>C synonymous_variant 0.12
rpoC 763768 c.399C>T synonymous_variant 0.12
rpoC 763774 c.405G>C synonymous_variant 0.11
rpoC 764339 c.970C>T synonymous_variant 0.13
rpoC 764365 c.996C>T synonymous_variant 0.12
rpoC 764371 c.1002G>T synonymous_variant 0.12
rpoC 764377 c.1008C>G synonymous_variant 0.12
rpoC 764380 c.1011G>C synonymous_variant 0.12
rpoC 764383 c.1014C>T synonymous_variant 0.12
rpoC 764387 c.1018T>C synonymous_variant 0.12
rpoC 764407 p.Arg346Ser missense_variant 0.11
rpoC 764497 c.1128A>G synonymous_variant 0.13
rpoC 764527 c.1158C>T synonymous_variant 0.14
rpoC 764530 c.1161C>T synonymous_variant 0.14
rpoC 764533 c.1164C>A synonymous_variant 0.14
rpoC 764536 c.1167G>T synonymous_variant 0.14
rpoC 764539 c.1170C>G synonymous_variant 0.13
rpoC 764548 c.1179G>A synonymous_variant 0.14
rpoC 764554 c.1185C>T synonymous_variant 0.14
rpoC 764566 c.1197C>G synonymous_variant 0.18
rpoC 764575 c.1206T>G synonymous_variant 0.2
rpoC 764578 c.1209C>G synonymous_variant 0.2
rpoC 764593 c.1224C>T synonymous_variant 0.17
rpoC 764602 c.1233C>T synonymous_variant 0.15
rpoC 764626 c.1257C>T synonymous_variant 0.15
rpoC 764632 c.1263T>C synonymous_variant 0.16
rpoC 764635 c.1266C>T synonymous_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.13
rpoC 764713 c.1344G>T synonymous_variant 0.26
rpoC 764746 c.1377G>T synonymous_variant 0.23
rpoC 764752 c.1383G>C synonymous_variant 0.17
rpoC 764758 c.1389C>G synonymous_variant 0.17
rpoC 764764 c.1395T>C synonymous_variant 0.17
rpoC 764803 c.1434C>T synonymous_variant 0.18
rpoC 764810 p.Pro481Ala missense_variant 0.15
rpoC 764815 c.1446A>G synonymous_variant 0.14
rpoC 764827 c.1458G>C synonymous_variant 0.14
rpoC 764858 c.1489T>C synonymous_variant 0.16
rpoC 764911 c.1542A>G synonymous_variant 0.11
rpoC 764912 p.Met515Leu missense_variant 0.1
rpoC 764932 c.1563C>A synonymous_variant 0.14
rpoC 764948 c.1579T>C synonymous_variant 0.12
rpoC 764968 c.1599T>C synonymous_variant 0.14
rpoC 765073 c.1704G>C synonymous_variant 0.12
rpoC 765449 p.Ala694Ser missense_variant 0.15
rpoC 765454 c.2085C>G synonymous_variant 0.15
rpoC 765469 c.2100G>C synonymous_variant 0.16
rpoC 765478 c.2109T>G synonymous_variant 0.18
rpoC 765480 p.Tyr704Phe missense_variant 0.18
rpoC 765496 c.2127C>T synonymous_variant 0.16
rpoC 765499 c.2130C>G synonymous_variant 0.16
rpoC 766645 p.Glu1092Asp missense_variant 1.0
rpoC 767080 c.3711G>C synonymous_variant 0.24
rpoC 767098 c.3729T>C synonymous_variant 0.33
rpoC 767100 p.Lys1244Arg missense_variant 0.33
rpoC 767104 c.3735C>G synonymous_variant 0.36
rpoC 767107 c.3738C>T synonymous_variant 0.36
rpoC 767119 c.3750A>G synonymous_variant 0.31
rpoC 767125 c.3756G>C synonymous_variant 0.25
rpoC 767134 c.3765C>T synonymous_variant 0.23
rpoC 767138 c.3769C>T synonymous_variant 0.23
rpoC 767149 c.3780C>T synonymous_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 1.0
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781829 c.270G>C synonymous_variant 0.12
rpsL 781832 c.273T>C synonymous_variant 0.11
fbiC 1304533 p.Leu535Ile missense_variant 0.12
fbiC 1304539 p.Arg537Ala missense_variant 0.12
fbiC 1304547 c.1617C>G synonymous_variant 0.12
fbiC 1304559 p.Glu543Asp missense_variant 0.12
fbiC 1304562 c.1632G>C synonymous_variant 0.12
fbiC 1304565 c.1635C>G synonymous_variant 0.11
fbiC 1304568 c.1638T>C synonymous_variant 0.11
fbiC 1304574 c.1644C>G synonymous_variant 0.12
fbiC 1304578 c.1648_1650delCGTinsAGG synonymous_variant 0.12
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
fabG1 1674049 p.Gln204Glu missense_variant 0.14
inhA 1674054 c.-148T>C upstream_gene_variant 0.14
inhA 1674060 c.-142A>G upstream_gene_variant 0.16
inhA 1674069 c.-133G>A upstream_gene_variant 0.16
inhA 1674072 c.-130C>G upstream_gene_variant 0.16
fabG1 1674079 p.Pro214Ala missense_variant 0.14
inhA 1674084 c.-118C>T upstream_gene_variant 0.14
inhA 1674592 p.Ala131Thr missense_variant 0.12
rpsA 1833790 c.249T>C synonymous_variant 0.11
rpsA 1833802 c.261A>G synonymous_variant 0.14
rpsA 1833811 c.270G>C synonymous_variant 0.14
rpsA 1833829 c.288A>G synonymous_variant 0.18
rpsA 1833832 c.291G>A synonymous_variant 0.18
rpsA 1833838 c.297G>T synonymous_variant 0.18
rpsA 1833841 c.300C>G synonymous_variant 0.19
rpsA 1833847 c.306C>G synonymous_variant 0.22
rpsA 1833856 c.315A>G synonymous_variant 0.18
rpsA 1833862 c.321G>T synonymous_variant 0.21
rpsA 1833874 c.333T>G synonymous_variant 0.23
rpsA 1833886 c.345C>G synonymous_variant 0.22
rpsA 1833892 c.351G>A synonymous_variant 0.19
rpsA 1833894 p.Ala118Glu missense_variant 0.19
rpsA 1833928 c.387G>C synonymous_variant 0.15
rpsA 1833934 c.393C>T synonymous_variant 0.17
rpsA 1833949 c.408T>C synonymous_variant 0.16
rpsA 1833970 c.429G>C synonymous_variant 0.12
rpsA 1834000 c.459G>C synonymous_variant 0.12
rpsA 1834021 c.480C>T synonymous_variant 0.12
rpsA 1834069 c.528G>C synonymous_variant 0.18
rpsA 1834073 p.Lys178Arg missense_variant 0.18
rpsA 1834097 c.556_557delTCinsAG synonymous_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 1.0
rpsA 1834228 c.687C>A synonymous_variant 0.16
rpsA 1834231 c.690T>G synonymous_variant 0.17
rpsA 1834234 c.693G>T synonymous_variant 0.17
rpsA 1834240 c.699T>C synonymous_variant 0.17
rpsA 1834246 c.705G>T synonymous_variant 0.15
rpsA 1834249 c.708T>C synonymous_variant 0.17
rpsA 1834252 c.711C>G synonymous_variant 0.15
rpsA 1834261 c.720A>G synonymous_variant 0.15
rpsA 1834264 c.723G>C synonymous_variant 0.15
rpsA 1834366 c.825A>G synonymous_variant 0.12
rpsA 1834375 c.834G>A synonymous_variant 0.17
rpsA 1834378 c.837T>C synonymous_variant 0.17
rpsA 1834396 c.855G>T synonymous_variant 0.18
rpsA 1834405 c.864C>T synonymous_variant 0.14
rpsA 1834408 c.867C>T synonymous_variant 0.14
rpsA 1834411 c.870T>C synonymous_variant 0.14
rpsA 1834417 c.876G>C synonymous_variant 0.14
rpsA 1834423 c.882G>C synonymous_variant 0.13
rpsA 1834435 c.894G>C synonymous_variant 0.13
rpsA 1834520 p.Ala327Ser missense_variant 0.18
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2102895 c.148C>T synonymous_variant 0.12
katG 2154724 p.Arg463Leu missense_variant 0.94
PPE35 2167926 p.Leu896Ser missense_variant 1.0
PPE35 2168432 c.2181G>A synonymous_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714478 c.855C>G synonymous_variant 0.11
Rv2752c 3065414 p.Ser260Thr missense_variant 0.14
thyA 3074022 c.450C>T synonymous_variant 0.22
thyA 3074031 c.441T>C synonymous_variant 0.2
thyA 3074037 c.435C>G synonymous_variant 0.15
thyA 3074045 c.427C>T synonymous_variant 0.13
thyA 3074056 p.Glu139Pro missense_variant 0.13
thyA 3074061 c.411A>G synonymous_variant 0.13
thyA 3074067 c.405C>G synonymous_variant 0.13
thyA 3074087 p.Ile129Val missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3449112 c.609T>C synonymous_variant 0.11
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
fprA 3474208 c.206delA frameshift_variant 0.14
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
Rv3236c 3613025 p.Ser31* stop_gained 0.12
rpoA 3877752 p.Asp252Glu missense_variant 0.12
rpoA 3877758 c.750G>C synonymous_variant 0.11
rpoA 3877764 c.744C>G synonymous_variant 0.1
rpoA 3877770 c.738A>G synonymous_variant 0.1
rpoA 3877773 c.735G>C synonymous_variant 0.12
rpoA 3877776 c.732T>C synonymous_variant 0.12
rpoA 3877782 c.726T>C synonymous_variant 0.12
rpoA 3877785 c.723C>A synonymous_variant 0.12
rpoA 3877818 c.690A>G synonymous_variant 0.17
rpoA 3878001 c.507A>G synonymous_variant 0.12
rpoA 3878061 c.447G>C synonymous_variant 0.15
rpoA 3878070 c.438T>C synonymous_variant 0.13
rpoA 3878079 c.429C>T synonymous_variant 0.13
rpoA 3878082 c.426T>C synonymous_variant 0.13
rpoA 3878143 p.Gly122Asp missense_variant 0.12
rpoA 3878193 c.315T>C synonymous_variant 0.11
rpoA 3878197 p.Glu104Ala missense_variant 0.11
rpoA 3878283 p.Glu75Asp missense_variant 0.11
rpoA 3878292 c.216T>C synonymous_variant 0.11
rpoA 3878298 c.210A>G synonymous_variant 0.11
rpoA 3878301 c.207C>G synonymous_variant 0.12
rpoA 3878310 c.198G>T synonymous_variant 0.12
rpoA 3878313 c.195G>C synonymous_variant 0.13
rpoA 3878322 c.186A>G synonymous_variant 0.11
rpoA 3878346 c.162T>C synonymous_variant 0.17
rpoA 3878364 c.144A>C synonymous_variant 0.2
rpoA 3878367 c.141C>G synonymous_variant 0.21
rpoA 3878370 c.138T>C synonymous_variant 0.21
rpoA 3878373 c.135G>C synonymous_variant 0.2
rpoA 3878391 c.117T>G synonymous_variant 0.13
rpoA 3878400 c.108T>C synonymous_variant 0.12
rpoA 3878424 c.84G>C synonymous_variant 0.14
rpoA 3878433 c.75G>C synonymous_variant 0.15
rpoA 3878436 c.72A>G synonymous_variant 0.11
rpoA 3878442 c.66G>C synonymous_variant 0.11
clpC1 4038842 c.1863G>T synonymous_variant 0.14
clpC1 4038845 c.1858_1860delTCGinsAGC synonymous_variant 0.14
clpC1 4038860 c.1845G>T synonymous_variant 0.14
clpC1 4038878 c.1827A>G synonymous_variant 0.12
clpC1 4039264 p.Asp481His missense_variant 0.12
clpC1 4039283 c.1422C>T synonymous_variant 0.11
clpC1 4039286 c.1419T>G synonymous_variant 0.15
clpC1 4039292 c.1413C>T synonymous_variant 0.18
clpC1 4039316 p.Glu463Asp missense_variant 0.19
clpC1 4039319 c.1386T>A synonymous_variant 0.19
clpC1 4039322 c.1383T>G synonymous_variant 0.18
clpC1 4039328 c.1377A>G synonymous_variant 0.2
clpC1 4039336 c.1369C>T synonymous_variant 0.17
clpC1 4039338 p.Thr456Gln missense_variant 0.15
clpC1 4039346 p.Arg453Ser missense_variant 0.21
clpC1 4039360 p.Ser449Arg missense_variant 0.24
clpC1 4039361 c.1344C>T synonymous_variant 0.24
clpC1 4039391 c.1314T>C synonymous_variant 0.12
clpC1 4039397 c.1308A>G synonymous_variant 0.12
clpC1 4039733 c.972G>C synonymous_variant 0.11
clpC1 4039739 c.966C>G synonymous_variant 0.14
clpC1 4039757 c.948A>G synonymous_variant 0.1
clpC1 4039769 c.936C>T synonymous_variant 0.12
clpC1 4039793 c.912C>G synonymous_variant 0.12
clpC1 4039805 c.900C>T synonymous_variant 0.12
clpC1 4040021 c.684A>C synonymous_variant 0.11
clpC1 4040033 c.672G>C synonymous_variant 0.12
clpC1 4040042 c.663C>T synonymous_variant 0.12
clpC1 4040057 c.648C>T synonymous_variant 0.12
clpC1 4040087 c.618G>T synonymous_variant 0.17
clpC1 4040090 c.613_615delTCTinsAGC synonymous_variant 0.17
clpC1 4040093 c.612C>G synonymous_variant 0.15
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
ethA 4326951 p.Ala175Ser missense_variant 0.18
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
gid 4408006 p.Val66Ala missense_variant 0.11