TB-Profiler result

Run: SRR13591342
Summary

Run ID: SRR13591342

Sample name:

Date: 03-04-2023 09:03:59

Number of reads: 1497232

Percentage reads mapped: 84.66

Strain: lineage4.1.1.3

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
lineage4 Euro-American LAM;T;S;X;H None 1.0
lineage4.1 Euro-American T;X;H None 0.97
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 0.99
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, 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 6919 c.-383T>C upstream_gene_variant 0.18
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8516 c.1215T>C synonymous_variant 0.18
gyrA 8762 c.1461G>C synonymous_variant 0.18
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491121 c.339A>G synonymous_variant 0.18
rpoB 760223 c.417T>C synonymous_variant 0.19
rpoB 760235 c.429T>C synonymous_variant 0.19
rpoB 760283 c.477G>C synonymous_variant 0.21
rpoB 760298 c.492G>C synonymous_variant 0.24
rpoB 760310 c.504G>C synonymous_variant 0.26
rpoB 760322 c.516G>A synonymous_variant 0.25
rpoB 760331 c.525G>C synonymous_variant 0.25
rpoB 760340 c.534G>C synonymous_variant 0.26
rpoB 760357 p.Thr184Ser missense_variant 0.25
rpoB 760361 c.555T>C synonymous_variant 0.23
rpoB 760370 c.564C>G synonymous_variant 0.23
rpoB 760376 p.Asp190Glu missense_variant 0.22
rpoB 760380 p.Thr192Leu missense_variant 0.23
rpoB 760418 c.612G>C synonymous_variant 0.22
rpoB 760424 c.618C>G synonymous_variant 0.21
rpoB 760430 c.624T>C synonymous_variant 0.2
rpoB 761765 c.1959T>C synonymous_variant 0.19
rpoB 761772 p.His656Ala missense_variant 0.19
rpoB 761778 p.Asn658Asp missense_variant 0.19
rpoB 761791 p.Arg662His missense_variant 0.19
rpoB 761813 c.2007T>C synonymous_variant 0.22
rpoB 761815 p.Ala670Glu missense_variant 0.21
rpoB 761834 c.2028T>C synonymous_variant 0.2
rpoB 762140 c.2334G>C synonymous_variant 0.18
rpoB 762161 c.2355C>G synonymous_variant 0.18
rpoB 762185 c.2379G>C synonymous_variant 0.19
rpoC 764431 c.1062G>C synonymous_variant 0.18
rpoC 764575 c.1206T>C synonymous_variant 0.18
rpoC 764632 c.1263T>C synonymous_variant 0.18
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 765734 c.2365_2367delTTGinsCTC synonymous_variant 0.19
rpoC 765739 c.2370G>C synonymous_variant 0.2
rpoC 765751 c.2382C>G synonymous_variant 0.21
rpoC 765753 p.Asp795Ala missense_variant 0.23
rpoC 765772 c.2403C>G synonymous_variant 0.21
rpoC 765784 c.2415C>G synonymous_variant 0.2
rpoC 765793 c.2424C>G synonymous_variant 0.2
rpoC 765796 c.2427C>T synonymous_variant 0.2
rpoC 765811 c.2442T>G synonymous_variant 0.21
rpoC 765826 c.2457T>C synonymous_variant 0.22
rpoC 765835 c.2466C>T synonymous_variant 0.22
rpoC 765850 c.2481G>C synonymous_variant 0.25
rpoC 765871 c.2502T>C synonymous_variant 0.21
rpoC 765883 c.2514C>G synonymous_variant 0.19
rpoC 765886 c.2517C>G synonymous_variant 0.2
rpoC 765892 c.2523T>C synonymous_variant 0.2
rpoC 766522 c.3153C>A synonymous_variant 0.2
rpoC 766525 c.3156G>T synonymous_variant 0.2
rpoC 766540 p.Asp1057Glu missense_variant 0.23
rpoC 766543 c.3174C>T synonymous_variant 0.21
rpoC 766549 c.3180G>C synonymous_variant 0.22
rpoC 766573 c.3204T>C synonymous_variant 0.25
rpoC 766582 c.3213C>G synonymous_variant 0.23
rpoC 766583 p.Gly1072Ser missense_variant 0.23
rpoC 766591 c.3222A>G synonymous_variant 0.24
rpoC 766594 c.3225G>C synonymous_variant 0.25
rpoC 766597 c.3228C>G synonymous_variant 0.25
rpoC 766607 p.Ile1080Leu missense_variant 0.28
rpoC 766645 c.3276A>G synonymous_variant 0.28
rpoC 766657 c.3288A>G synonymous_variant 0.29
rpoC 766660 c.3291G>A synonymous_variant 0.29
rpoC 766666 c.3297C>T synonymous_variant 0.26
rpoC 766672 c.3303T>C synonymous_variant 0.25
rpoC 766693 c.3324C>T synonymous_variant 0.25
rpoC 766726 c.3357T>C synonymous_variant 0.25
rpoC 766733 c.3364C>T synonymous_variant 0.24
rpoC 766738 c.3369G>C synonymous_variant 0.19
rpoC 766765 c.3396A>C synonymous_variant 0.2
rpoC 766774 c.3405T>C synonymous_variant 0.22
rpoC 766801 c.3432C>T synonymous_variant 0.22
rpoC 766804 c.3435A>G synonymous_variant 0.25
rpoC 766837 c.3468G>C synonymous_variant 0.27
rpoC 766864 c.3495G>C synonymous_variant 0.25
rpoC 766894 c.3525T>C synonymous_variant 0.27
rpoC 766895 c.3526T>C synonymous_variant 0.26
rpoC 766900 c.3531T>C synonymous_variant 0.27
rpoC 766918 c.3549C>T synonymous_variant 0.26
rpoC 766933 c.3564A>G synonymous_variant 0.23
rpoC 766934 p.Glu1189Ser missense_variant 0.22
rpoC 766945 c.3576A>C synonymous_variant 0.24
rpoC 766963 c.3594T>C synonymous_variant 0.24
rpoC 766972 c.3603G>C synonymous_variant 0.25
rpoC 766978 c.3609C>T synonymous_variant 0.22
rpoC 766996 c.3627C>T synonymous_variant 0.23
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.2
rpoC 767014 c.3645G>C synonymous_variant 0.2
rpoC 767035 c.3666G>C synonymous_variant 0.21
rpoC 767059 c.3690T>G synonymous_variant 0.21
mmpL5 775639 p.Ile948Val missense_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781760 c.201T>C synonymous_variant 0.17
rpsL 781793 c.234G>C synonymous_variant 0.19
rpsL 781832 c.273T>G synonymous_variant 0.2
fbiC 1303331 p.Arg134Gln missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.2
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.2
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.24
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.19
rrl 1473840 n.183A>G non_coding_transcript_exon_variant 0.22
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.21
rrl 1473898 n.241C>T non_coding_transcript_exon_variant 0.24
rrl 1473917 n.260G>A non_coding_transcript_exon_variant 0.22
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.23
rrl 1473945 n.288T>A non_coding_transcript_exon_variant 0.23
rrl 1473946 n.289A>T non_coding_transcript_exon_variant 0.23
rrl 1473986 n.329T>C non_coding_transcript_exon_variant 0.24
rrl 1473987 n.330G>A non_coding_transcript_exon_variant 0.23
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.23
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.22
rrl 1474009 n.352A>G non_coding_transcript_exon_variant 0.22
rrl 1474012 n.355C>T non_coding_transcript_exon_variant 0.23
rrl 1474049 n.392G>A non_coding_transcript_exon_variant 0.2
rrl 1474093 n.436G>T non_coding_transcript_exon_variant 0.2
rrl 1474099 n.442G>A non_coding_transcript_exon_variant 0.2
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.2
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.19
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.22
rrl 1474201 n.544T>C non_coding_transcript_exon_variant 0.23
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.25
rrl 1474291 n.635_649delTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.25
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.24
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.22
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.24
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.23
rrl 1474376 n.719T>C non_coding_transcript_exon_variant 0.22
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.23
rrl 1474961 n.1304T>G non_coding_transcript_exon_variant 0.22
rrl 1474963 n.1306G>A non_coding_transcript_exon_variant 0.22
rrl 1474964 n.1307T>C non_coding_transcript_exon_variant 0.21
rrl 1474970 n.1313G>A non_coding_transcript_exon_variant 0.21
rrl 1475006 n.1349A>T non_coding_transcript_exon_variant 0.23
rrl 1475028 n.1371G>A non_coding_transcript_exon_variant 0.26
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.25
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.29
rrl 1475199 n.1542G>A non_coding_transcript_exon_variant 0.28
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.27
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.3
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.3
rrl 1475249 n.1592T>C non_coding_transcript_exon_variant 0.27
rrl 1475252 n.1595C>T non_coding_transcript_exon_variant 0.26
rrl 1475266 n.1609T>C non_coding_transcript_exon_variant 0.29
rrl 1475273 n.1616T>G non_coding_transcript_exon_variant 0.29
rrl 1475275 n.1618C>T non_coding_transcript_exon_variant 0.29
rrl 1475276 n.1619T>C non_coding_transcript_exon_variant 0.29
rrl 1475279 n.1622G>C non_coding_transcript_exon_variant 0.29
rrl 1475291 n.1634A>C non_coding_transcript_exon_variant 0.28
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.27
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.28
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.26
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.2
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.19
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.19
inhA 1674600 c.399G>T synonymous_variant 0.19
rpsA 1833787 c.246C>G synonymous_variant 0.19
rpsA 1833790 c.249T>A synonymous_variant 0.19
rpsA 1833811 c.270G>C synonymous_variant 0.18
rpsA 1834246 c.705G>C synonymous_variant 0.19
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289017 c.225T>C synonymous_variant 1.0
kasA 2518609 p.Met165Ile missense_variant 0.19
kasA 2518618 c.504G>T synonymous_variant 0.2
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.98
fbiA 3641038 p.Ala166Thr missense_variant 1.0
rpoA 3878094 c.412_414delCTCinsTTG synonymous_variant 0.2
rpoA 3878100 c.408C>G synonymous_variant 0.21
rpoA 3878106 c.402G>C synonymous_variant 0.2
rpoA 3878118 c.390T>C synonymous_variant 0.2
rpoA 3878130 c.378C>G synonymous_variant 0.2
rpoA 3878141 p.Met123Leu missense_variant 0.2
rpoA 3878142 p.Gly122Glu missense_variant 0.2
rpoA 3878157 c.351C>G synonymous_variant 0.2
rpoA 3878163 c.345C>T synonymous_variant 0.22
rpoA 3878169 c.339G>C synonymous_variant 0.22
rpoA 3878172 c.336G>C synonymous_variant 0.24
rpoA 3878187 c.321C>A synonymous_variant 0.23
rpoA 3878193 c.315T>C synonymous_variant 0.21
rpoA 3878197 p.Glu104Ala missense_variant 0.23
rpoA 3878205 c.303T>C synonymous_variant 0.22
rpoA 3878217 c.291A>G synonymous_variant 0.21
rpoA 3878220 c.288C>T synonymous_variant 0.2
rpoA 3878247 c.261G>C synonymous_variant 0.19
rpoA 3878253 c.255G>C synonymous_variant 0.2
rpoA 3878271 c.237T>C synonymous_variant 0.21
rpoA 3878284 p.Glu75Ala missense_variant 0.18
rpoA 3878292 c.216T>C synonymous_variant 0.19
rpoA 3878298 c.210A>G synonymous_variant 0.19
rpoA 3878313 c.195G>C synonymous_variant 0.18
rpoA 3878337 c.171T>C synonymous_variant 0.19
rpoA 3878346 c.162T>C synonymous_variant 0.21
rpoA 3878361 c.147G>C synonymous_variant 0.22
rpoA 3878364 c.144A>C synonymous_variant 0.22
rpoA 3878367 c.141C>G synonymous_variant 0.23
rpoA 3878376 c.132G>C synonymous_variant 0.2
rpoA 3878385 c.123C>G synonymous_variant 0.2
rpoA 3878388 c.120C>G synonymous_variant 0.2
rpoA 3878391 c.117T>C synonymous_variant 0.2
rpoA 3878396 c.112C>T synonymous_variant 0.2
rpoA 3878415 c.93C>T synonymous_variant 0.21
rpoA 3878442 c.66G>C synonymous_variant 0.17
rpoA 3878454 c.54A>C synonymous_variant 0.21
clpC1 4038755 c.1950G>T synonymous_variant 0.19
clpC1 4038773 c.1932T>C synonymous_variant 0.23
clpC1 4038782 c.1923G>C synonymous_variant 0.22
clpC1 4038790 c.1915C>T synonymous_variant 0.23
clpC1 4038812 c.1893T>C synonymous_variant 0.23
clpC1 4038845 c.1860G>C synonymous_variant 0.25
clpC1 4038848 c.1857C>T synonymous_variant 0.25
clpC1 4038860 c.1845G>C synonymous_variant 0.24
clpC1 4038878 c.1827A>G synonymous_variant 0.21
clpC1 4039226 c.1479T>C synonymous_variant 0.19
clpC1 4039268 c.1437C>G synonymous_variant 0.19
clpC1 4039280 c.1425G>C synonymous_variant 0.19
clpC1 4039286 c.1419T>C synonymous_variant 0.18
clpC1 4039349 c.1356C>T synonymous_variant 0.18
clpC1 4039364 c.1341C>G synonymous_variant 0.2
clpC1 4039391 c.1314T>G synonymous_variant 0.2
clpC1 4039397 c.1308A>G synonymous_variant 0.2
clpC1 4039409 c.1296T>C synonymous_variant 0.2
clpC1 4039439 c.1266C>T synonymous_variant 0.2
clpC1 4039442 c.1263A>G synonymous_variant 0.2
clpC1 4039454 c.1251A>G synonymous_variant 0.23
clpC1 4039463 c.1242C>G synonymous_variant 0.21
clpC1 4039466 c.1239T>C synonymous_variant 0.22
clpC1 4039469 c.1236T>C synonymous_variant 0.22
clpC1 4039481 c.1224T>C synonymous_variant 0.26
clpC1 4039484 c.1221T>C synonymous_variant 0.24
clpC1 4039517 c.1188C>G synonymous_variant 0.21
clpC1 4039541 c.1164C>T synonymous_variant 0.2
clpC1 4039556 c.1149G>C synonymous_variant 0.21
clpC1 4039559 c.1146C>G synonymous_variant 0.21
clpC1 4039562 c.1143C>G synonymous_variant 0.2
clpC1 4039565 c.1140G>C synonymous_variant 0.21
clpC1 4039570 p.Met379Leu missense_variant 0.21
clpC1 4039571 c.1134G>A synonymous_variant 0.2
clpC1 4039576 p.Ala377Pro missense_variant 0.2
clpC1 4039577 c.1128T>C synonymous_variant 0.21
clpC1 4039586 c.1119G>C synonymous_variant 0.2
clpC1 4039601 c.1104G>A synonymous_variant 0.2
clpC1 4039610 c.1095G>C synonymous_variant 0.2
clpC1 4040267 c.438A>G synonymous_variant 0.2
clpC1 4040278 p.Ser143Thr missense_variant 0.18
clpC1 4040279 c.426C>G synonymous_variant 0.18
clpC1 4040291 c.414G>C synonymous_variant 0.18
embC 4240819 c.957A>G synonymous_variant 0.2
embC 4240828 c.966G>C synonymous_variant 0.2
embA 4242643 c.-590C>T upstream_gene_variant 0.92
embC 4242803 p.Val981Leu missense_variant 0.86
embB 4249408 c.2895G>A synonymous_variant 0.96
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407714 p.Lys163Asn missense_variant 0.98