TB-Profiler result

Run: SRR13861396
Summary

Run ID: SRR13861396

Sample name:

Date: 03-04-2023 09:30:54

Number of reads: 2019603

Percentage reads mapped: 67.39

Strain: lineage4.9

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
lineage4.9 Euro-American (H37Rv-like) T1 None 1.0
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 2154798 c.1313_1314insT frameshift_variant 1.0 isoniazid
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 5906 p.Val223Leu missense_variant 1.0
gyrB 6011 p.Val258Met missense_variant 1.0
gyrB 6678 p.Pro480Arg missense_variant 0.9
gyrA 7523 c.222C>G synonymous_variant 0.16
gyrA 7532 c.231T>C synonymous_variant 0.14
gyrA 7541 c.240C>G synonymous_variant 0.15
gyrA 8111 c.810G>C synonymous_variant 0.16
gyrA 8168 c.867A>G synonymous_variant 0.15
gyrA 8174 c.873C>G synonymous_variant 0.14
gyrA 8177 c.876A>C synonymous_variant 0.15
gyrA 8198 c.897T>C synonymous_variant 0.15
gyrA 8375 c.1074G>C synonymous_variant 0.14
gyrA 8399 c.1098T>C synonymous_variant 0.15
gyrA 8442 c.1141C>T synonymous_variant 0.14
gyrA 8453 c.1152A>C synonymous_variant 0.16
gyrA 8462 c.1161A>G synonymous_variant 0.15
gyrA 8471 c.1170T>C synonymous_variant 0.17
gyrA 8480 c.1179C>T synonymous_variant 0.16
gyrA 8486 c.1185T>C synonymous_variant 0.14
gyrA 8498 c.1197C>T synonymous_variant 0.16
gyrA 8504 c.1203G>C synonymous_variant 0.16
gyrA 8516 c.1215T>C synonymous_variant 0.16
gyrA 8519 c.1218A>C synonymous_variant 0.17
gyrA 8537 c.1236G>A synonymous_variant 0.16
gyrA 8546 c.1245T>C synonymous_variant 0.16
gyrA 8552 c.1251C>G synonymous_variant 0.16
gyrA 8556 p.Ala419Gln missense_variant 0.15
gyrA 8561 c.1260A>C synonymous_variant 0.15
gyrA 8562 c.1261C>T synonymous_variant 0.14
gyrA 8619 c.1318T>C synonymous_variant 0.16
gyrA 8636 c.1335A>G synonymous_variant 0.15
gyrA 8642 c.1341A>G synonymous_variant 0.15
gyrA 8645 c.1344C>G synonymous_variant 0.15
fgd1 490676 c.-107G>C upstream_gene_variant 1.0
fgd1 491244 c.462T>C synonymous_variant 0.15
mshA 575649 p.Val101Glu missense_variant 0.14
ccsA 620028 c.138G>C synonymous_variant 1.0
rpoB 759638 c.-169T>A upstream_gene_variant 0.97
rpoB 760235 c.429T>C synonymous_variant 0.16
rpoB 760454 c.650delG frameshift_variant 0.95
rpoB 761150 c.1344A>C synonymous_variant 0.16
rpoB 761165 c.1359G>C synonymous_variant 0.14
rpoB 761171 c.1365C>T synonymous_variant 0.14
rpoB 761222 c.1416G>C synonymous_variant 0.16
rpoB 761255 c.1449T>G synonymous_variant 0.16
rpoB 761261 c.1455G>T synonymous_variant 0.17
rpoC 762989 c.-381G>C upstream_gene_variant 0.19
rpoC 762995 c.-375G>T upstream_gene_variant 0.18
rpoC 763028 c.-342T>C upstream_gene_variant 0.19
rpoC 763031 c.-339T>G upstream_gene_variant 0.19
rpoC 763034 c.-336C>G upstream_gene_variant 0.19
rpoC 763040 c.-330C>G upstream_gene_variant 0.19
rpoC 763158 c.-212C>T upstream_gene_variant 0.15
rpoC 763858 c.489A>G synonymous_variant 0.17
rpoC 763872 p.Gly168Ala missense_variant 0.16
rpoC 763876 p.Glu169Asp missense_variant 0.15
rpoC 763879 c.510A>G synonymous_variant 0.15
rpoC 763888 c.519G>C synonymous_variant 0.15
rpoC 763891 c.522G>C synonymous_variant 0.15
rpoC 763894 c.525A>G synonymous_variant 0.15
rpoC 763919 c.550C>T synonymous_variant 0.16
rpoC 763933 c.564C>T synonymous_variant 0.14
rpoC 764161 c.792G>C synonymous_variant 0.14
rpoC 764196 p.Ser276* stop_gained 0.14
rpoC 764560 c.1191T>C synonymous_variant 0.14
rpoC 764650 c.1281G>T synonymous_variant 0.14
rpoC 764791 c.1422C>G synonymous_variant 0.15
rpoC 764893 c.1524T>C synonymous_variant 0.15
rpoC 765487 p.Met706Ile missense_variant 0.91
rpoC 765658 c.2289C>T synonymous_variant 0.12
rpoC 765700 c.2331T>C synonymous_variant 0.15
rpoC 765734 c.2365T>C synonymous_variant 0.17
rpoC 765739 c.2370G>C synonymous_variant 0.17
rpoC 765751 c.2382C>G synonymous_variant 0.16
rpoC 765753 p.Asp795Ala missense_variant 0.16
rpoC 765772 c.2403C>G synonymous_variant 0.16
rpoC 765784 c.2415C>G synonymous_variant 0.17
rpoC 765796 c.2427C>T synonymous_variant 0.18
rpoC 765835 c.2466C>T synonymous_variant 0.13
rpoC 765928 c.2559C>G synonymous_variant 0.17
rpoC 765970 c.2601C>T synonymous_variant 0.13
rpoC 765982 c.2613C>T synonymous_variant 0.13
rpoC 765985 c.2616C>T synonymous_variant 0.15
rpoC 766010 p.Ser881Thr missense_variant 0.13
rpoC 766996 c.3627C>T synonymous_variant 0.13
rpoC 767035 c.3666G>T synonymous_variant 0.13
rpoC 767059 c.3690T>G synonymous_variant 0.15
rpoC 767062 c.3693C>A synonymous_variant 0.15
rpoC 767119 c.3750A>G synonymous_variant 0.16
rpoC 767158 c.3789T>C synonymous_variant 0.18
rpoC 767167 c.3798C>G synonymous_variant 0.15
rpoC 767181 p.Ala1271Glu missense_variant 0.15
rpsL 781409 c.-151T>A upstream_gene_variant 1.0
rpsL 781793 c.234G>C synonymous_variant 0.15
rpsL 781841 c.282C>G synonymous_variant 0.16
rpsL 781859 c.300T>C synonymous_variant 0.14
rpsL 781868 c.309T>C synonymous_variant 0.14
rpsL 781892 c.333A>G synonymous_variant 0.16
rpsL 781898 c.339A>T synonymous_variant 0.16
rpsL 781916 c.357T>C synonymous_variant 0.15
rpsL 781929 p.Gly124Ser missense_variant 0.18
rplC 800612 c.-197A>G upstream_gene_variant 0.18
rplC 800618 c.-191T>C upstream_gene_variant 0.17
rplC 800648 c.-161A>C upstream_gene_variant 0.21
rplC 800654 c.-155T>C upstream_gene_variant 0.17
rplC 800715 c.-94A>C upstream_gene_variant 0.17
rplC 800747 c.-62C>G upstream_gene_variant 0.16
rplC 800771 c.-38C>T upstream_gene_variant 0.2
rplC 800814 c.6A>G synonymous_variant 0.21
rplC 800817 c.9A>T synonymous_variant 0.21
rplC 800844 c.36T>C synonymous_variant 0.19
rplC 800865 c.57A>G synonymous_variant 0.15
rplC 800867 p.Ser20Asn missense_variant 0.15
rplC 800874 c.66A>G synonymous_variant 0.15
rplC 800877 c.69A>C synonymous_variant 0.14
rplC 800880 c.72A>G synonymous_variant 0.15
rplC 800889 c.81C>G synonymous_variant 0.18
rplC 800907 c.99C>G synonymous_variant 0.14
rplC 800916 c.108A>G synonymous_variant 0.15
rplC 801301 c.493C>A synonymous_variant 0.14
rplC 801312 c.504G>C synonymous_variant 0.15
rplC 801324 c.516T>C synonymous_variant 0.14
fbiC 1302873 c.-58A>T upstream_gene_variant 1.0
fbiC 1304517 c.1587C>T synonymous_variant 0.13
fbiC 1304523 c.1593G>T synonymous_variant 0.13
fbiC 1304565 c.1635C>G synonymous_variant 0.16
fbiC 1304568 c.1638T>C synonymous_variant 0.18
fbiC 1304574 c.1644C>G synonymous_variant 0.2
fbiC 1304580 c.1650T>C synonymous_variant 0.22
fbiC 1304628 c.1698G>C synonymous_variant 0.23
fbiC 1304634 c.1704C>G synonymous_variant 0.25
fbiC 1304640 c.1710A>C synonymous_variant 0.23
fbiC 1304646 c.1716T>C synonymous_variant 0.21
fbiC 1304658 c.1728C>G synonymous_variant 0.22
fbiC 1304670 c.1740G>T synonymous_variant 0.2
fbiC 1304671 p.Val581Thr missense_variant 0.21
fbiC 1304675 p.Gly582Glu missense_variant 0.21
fbiC 1304691 c.1761G>C synonymous_variant 0.26
fbiC 1304694 c.1764A>C synonymous_variant 0.26
fbiC 1304703 c.1773C>G synonymous_variant 0.27
fbiC 1304715 c.1785G>C synonymous_variant 0.24
fbiC 1304724 c.1794A>G synonymous_variant 0.21
fbiC 1304727 c.1797A>G synonymous_variant 0.2
fbiC 1304742 c.1812T>C synonymous_variant 0.16
fbiC 1304748 c.1818T>C synonymous_variant 0.16
fbiC 1304754 c.1824G>A synonymous_variant 0.16
fbiC 1304757 c.1827A>G synonymous_variant 0.18
fbiC 1304784 c.1854T>C synonymous_variant 0.18
fbiC 1304787 c.1857T>C synonymous_variant 0.18
fbiC 1304790 c.1860C>G synonymous_variant 0.17
fbiC 1304808 c.1878C>G synonymous_variant 0.16
fbiC 1304811 c.1881C>G synonymous_variant 0.16
fbiC 1304817 c.1887T>C synonymous_variant 0.17
rrs 1471874 n.29A>C non_coding_transcript_exon_variant 0.93
rrs 1472028 n.183A>T non_coding_transcript_exon_variant 0.15
rrs 1472030 n.185G>A non_coding_transcript_exon_variant 0.15
rrs 1472031 n.186G>A non_coding_transcript_exon_variant 0.16
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.16
rrs 1472044 n.199G>C non_coding_transcript_exon_variant 0.16
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.16
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.15
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.15
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.15
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.17
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.15
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.21
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.19
rrl 1474823 n.1166C>T non_coding_transcript_exon_variant 0.18
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.18
rrl 1474904 n.1247G>A non_coding_transcript_exon_variant 0.18
rrl 1475088 n.1431A>T non_coding_transcript_exon_variant 0.14
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.14
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.15
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.17
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.18
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.17
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.18
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.21
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.19
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.16
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.15
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.15
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.15
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.15
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.15
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.18
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.18
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.17
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.17
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.17
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.17
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.19
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.21
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.18
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.17
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.18
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.18
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.15
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.16
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.2
inhA 1674582 c.381T>C synonymous_variant 0.14
inhA 1674654 c.453G>C synonymous_variant 0.14
rpsA 1834411 c.870T>C synonymous_variant 0.14
katG 2154654 p.Ser486Arg missense_variant 1.0
katG 2154882 c.1230G>A synonymous_variant 1.0
katG 2155857 c.255C>A synonymous_variant 0.98
PPE35 2170198 p.Ala139Ser missense_variant 1.0
pncA 2290069 c.-828C>T upstream_gene_variant 1.0
kasA 2518687 c.573C>T synonymous_variant 0.14
kasA 2518702 c.588C>T synonymous_variant 0.14
kasA 2518717 c.603C>T synonymous_variant 0.14
kasA 2518723 p.Glu203Asp missense_variant 0.14
kasA 2518732 c.618C>G synonymous_variant 0.16
kasA 2518741 c.627G>C synonymous_variant 0.16
kasA 2518747 c.633C>G synonymous_variant 0.17
kasA 2518768 c.654C>G synonymous_variant 0.17
kasA 2518783 c.669T>C synonymous_variant 0.18
kasA 2518792 c.678C>G synonymous_variant 0.17
kasA 2518795 c.681C>G synonymous_variant 0.16
eis 2714922 c.411G>A synonymous_variant 1.0
folC 2747355 p.Val82Ile missense_variant 0.13
thyX 3067787 c.159G>A synonymous_variant 0.16
thyX 3067793 c.153T>C synonymous_variant 0.15
thyX 3067799 c.147G>A synonymous_variant 0.14
thyX 3067814 c.132T>C synonymous_variant 0.16
thyX 3067826 c.120C>G synonymous_variant 0.16
thyA 3074067 c.405C>G synonymous_variant 0.92
alr 3840223 c.1198A>C synonymous_variant 1.0
alr 3840711 p.Ser237Leu missense_variant 1.0
rpoA 3877857 c.651G>A synonymous_variant 0.15
rpoA 3877866 c.642G>C synonymous_variant 0.15
rpoA 3877872 c.636C>T synonymous_variant 0.15
rpoA 3877875 c.633T>G synonymous_variant 0.15
rpoA 3878070 c.438T>C synonymous_variant 0.15
rpoA 3878082 c.426T>C synonymous_variant 0.17
rpoA 3878094 c.414C>G synonymous_variant 0.17
rpoA 3878100 c.408C>G synonymous_variant 0.17
rpoA 3878103 c.405A>G synonymous_variant 0.17
rpoA 3878106 c.402G>C synonymous_variant 0.19
rpoA 3878118 c.390T>C synonymous_variant 0.18
rpoA 3878141 p.Met123Leu missense_variant 0.2
rpoA 3878142 p.Gly122Glu missense_variant 0.19
rpoA 3878169 c.339G>C synonymous_variant 0.21
rpoA 3878184 c.324C>T synonymous_variant 0.19
rpoA 3878187 c.321C>G synonymous_variant 0.19
rpoA 3878193 c.315T>C synonymous_variant 0.19
rpoA 3878199 c.309T>C synonymous_variant 0.19
rpoA 3878202 c.306G>C synonymous_variant 0.19
rpoA 3878217 c.291A>G synonymous_variant 0.22
rpoA 3878220 c.288C>T synonymous_variant 0.2
rpoA 3878271 c.237T>C synonymous_variant 0.23
rpoA 3878284 p.Glu75Ala missense_variant 0.23
rpoA 3878292 c.216T>C synonymous_variant 0.23
rpoA 3878298 c.210A>G synonymous_variant 0.23
rpoA 3878304 c.204G>C synonymous_variant 0.21
rpoA 3878313 c.195G>C synonymous_variant 0.2
rpoA 3878322 c.186A>G synonymous_variant 0.21
rpoA 3878331 c.177A>G synonymous_variant 0.22
rpoA 3878334 c.174T>C synonymous_variant 0.21
rpoA 3878337 c.171T>C synonymous_variant 0.21
rpoA 3878346 c.162T>C synonymous_variant 0.21
rpoA 3878364 c.144A>G synonymous_variant 0.19
rpoA 3878367 c.141C>G synonymous_variant 0.18
rpoA 3878370 c.138T>C synonymous_variant 0.19
rpoA 3878376 c.132G>C synonymous_variant 0.18
rpoA 3878385 c.123C>G synonymous_variant 0.17
rpoA 3878391 c.117T>C synonymous_variant 0.18
rpoA 3878396 c.112C>T synonymous_variant 0.16
clpC1 4038653 c.2052C>T synonymous_variant 0.13
clpC1 4038661 p.Ser682Thr missense_variant 0.13
clpC1 4038740 c.1965G>C synonymous_variant 0.17
clpC1 4038748 p.Arg653Cys missense_variant 0.18
clpC1 4038755 c.1950G>C synonymous_variant 0.18
clpC1 4038773 c.1932T>C synonymous_variant 0.19
clpC1 4038782 c.1923G>C synonymous_variant 0.18
clpC1 4038790 c.1915C>T synonymous_variant 0.2
clpC1 4038812 c.1893T>C synonymous_variant 0.17
clpC1 4038815 c.1890G>T synonymous_variant 0.16
clpC1 4038851 c.1854G>A synonymous_variant 0.2
clpC1 4038878 c.1827A>G synonymous_variant 0.22
clpC1 4038908 c.1797C>G synonymous_variant 0.18
clpC1 4038914 c.1791G>C synonymous_variant 0.17
clpC1 4038923 c.1782A>G synonymous_variant 0.17
clpC1 4038932 c.1773G>C synonymous_variant 0.18
clpC1 4038953 c.1752A>G synonymous_variant 0.17
clpC1 4038956 c.1749T>C synonymous_variant 0.18
clpC1 4038965 c.1740T>C synonymous_variant 0.19
clpC1 4038971 c.1734T>C synonymous_variant 0.19
clpC1 4038974 c.1731T>C synonymous_variant 0.21
clpC1 4038989 c.1716T>C synonymous_variant 0.17
clpC1 4038997 c.1708T>C synonymous_variant 0.17
clpC1 4039022 c.1683A>G synonymous_variant 0.15
clpC1 4039616 c.1089G>C synonymous_variant 0.15
clpC1 4039648 p.Glu353Gln missense_variant 0.85
clpC1 4039682 c.1023C>G synonymous_variant 0.15
clpC1 4039685 c.1020C>T synonymous_variant 0.15
clpC1 4039694 c.1011G>C synonymous_variant 0.16
clpC1 4040423 c.282A>G synonymous_variant 0.15
clpC1 4040426 c.279T>C synonymous_variant 0.15
clpC1 4040431 c.274T>C synonymous_variant 0.15
clpC1 4040465 c.240T>C synonymous_variant 0.16
clpC1 4040471 c.234T>C synonymous_variant 0.14
clpC1 4040477 c.228G>A synonymous_variant 0.14
embC 4240780 c.918T>C synonymous_variant 0.16
embC 4240783 c.921G>C synonymous_variant 0.15
embC 4240789 c.927T>C synonymous_variant 0.15
embC 4240819 c.957A>G synonymous_variant 0.15
embC 4241017 c.1155T>C synonymous_variant 0.15
embC 4241023 c.1161T>G synonymous_variant 0.15
embC 4241026 c.1164C>G synonymous_variant 0.15
embC 4241035 c.1173G>A synonymous_variant 0.17
embC 4241050 c.1188T>G synonymous_variant 0.14
embC 4242023 p.Val721Leu missense_variant 1.0
embA 4245071 c.1839G>A synonymous_variant 0.93
ethA 4327364 p.Lys37Arg missense_variant 1.0