TB-Profiler result

Run: SRR6981961
Summary

Run ID: SRR6981961

Sample name:

Date: 04-04-2023 18:23:12

Number of reads: 435058

Percentage reads mapped: 91.07

Strain: lineage2.2.1

Drug-resistance: Sensitive

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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 0.99
lineage2.2 East-Asian (Beijing) Beijing-RD207 RD105;RD207 0.99
lineage2.2.1 East-Asian (Beijing) Beijing-RD181 RD105;RD207;RD181 0.98
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
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 7499 c.198G>A synonymous_variant 0.13
gyrA 7523 c.222C>A synonymous_variant 0.13
gyrA 7526 c.225G>T synonymous_variant 0.14
gyrA 7532 c.231T>C synonymous_variant 0.14
gyrA 7541 c.240C>G synonymous_variant 0.14
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 7595 c.294C>G synonymous_variant 0.12
gyrA 7614 c.313C>T synonymous_variant 0.17
gyrA 7865 c.564T>C synonymous_variant 0.13
gyrA 7886 c.585T>C synonymous_variant 0.11
gyrA 7889 c.588G>A synonymous_variant 0.12
gyrA 7890 c.589C>T synonymous_variant 0.12
gyrA 7898 p.Asp199Glu missense_variant 0.12
gyrA 8339 c.1038A>G synonymous_variant 0.12
gyrA 8340 p.Ala347Ser missense_variant 0.12
gyrA 8375 c.1074G>C synonymous_variant 0.14
gyrA 8382 p.Leu361Met missense_variant 0.12
gyrA 8391 p.Tyr364His missense_variant 0.12
gyrA 8399 c.1098T>C synonymous_variant 0.13
gyrA 8401 p.Asp367Ala missense_variant 0.12
gyrA 8414 c.1113C>T synonymous_variant 0.12
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491742 c.960T>C synonymous_variant 1.0
mshA 575728 c.381C>A synonymous_variant 0.12
mshA 575734 c.387T>G synonymous_variant 0.12
mshA 575737 c.390T>C synonymous_variant 0.12
mshA 575744 p.Ala133Thr missense_variant 0.12
mshA 575749 c.402C>G synonymous_variant 0.12
mshA 575756 c.409C>T synonymous_variant 0.12
mshA 575764 c.417C>A synonymous_variant 0.12
mshA 575771 p.Val142Thr missense_variant 0.12
mshA 575779 c.432A>G synonymous_variant 0.13
mshA 575782 c.435G>C synonymous_variant 0.13
mshA 575785 c.438T>C synonymous_variant 0.12
mshA 575907 p.Ala187Val missense_variant 1.0
mshA 576450 p.Pro368Gln missense_variant 0.11
ccsA 620625 p.Ile245Met missense_variant 1.0
rpoB 760283 c.477G>C synonymous_variant 0.15
rpoB 760298 c.492G>C synonymous_variant 0.17
rpoB 760310 c.504G>C synonymous_variant 0.18
rpoB 760316 c.510C>G synonymous_variant 0.19
rpoB 760325 c.519G>C synonymous_variant 0.2
rpoB 760331 c.525G>C synonymous_variant 0.17
rpoB 760334 c.528G>T synonymous_variant 0.15
rpoB 760340 c.534G>T synonymous_variant 0.21
rpoB 760357 p.Thr184Ser missense_variant 0.19
rpoB 760361 c.555T>C synonymous_variant 0.2
rpoB 760370 c.564C>G synonymous_variant 0.19
rpoB 760376 p.Asp190Glu missense_variant 0.19
rpoB 760407 p.Ser201Gly missense_variant 0.2
rpoB 760415 c.609C>T synonymous_variant 0.2
rpoB 760424 c.618C>G synonymous_variant 0.2
rpoB 760430 c.624T>C synonymous_variant 0.22
rpoB 760457 c.651C>T synonymous_variant 0.17
rpoB 760460 c.654G>C synonymous_variant 0.19
rpoB 760475 c.669A>G synonymous_variant 0.18
rpoB 760478 c.672C>T synonymous_variant 0.18
rpoB 760481 c.675G>T synonymous_variant 0.17
rpoB 760484 c.678A>G synonymous_variant 0.17
rpoB 760502 c.696C>G synonymous_variant 0.18
rpoB 760561 c.757_758delCG frameshift_variant 0.12
rpoB 760567 p.Ser254Trp missense_variant 0.12
rpoB 760568 c.762_763insGC frameshift_variant 0.12
rpoB 760571 c.765G>C synonymous_variant 0.12
rpoB 760574 c.768G>C synonymous_variant 0.12
rpoB 760585 p.Asn260Ser missense_variant 0.13
rpoB 760591 p.Val262Ala missense_variant 0.15
rpoB 760596 p.Thr264Pro missense_variant 0.21
rpoB 760611 c.805T>C synonymous_variant 0.18
rpoB 760625 c.819C>G synonymous_variant 0.18
rpoB 760646 c.840C>G synonymous_variant 0.16
rpoB 760655 c.849A>G synonymous_variant 0.16
rpoB 760661 c.855A>C synonymous_variant 0.16
rpoB 760670 c.864G>C synonymous_variant 0.16
rpoB 760683 c.877T>C synonymous_variant 0.11
rpoB 761345 c.1539G>T synonymous_variant 0.11
rpoB 762101 c.2295C>G synonymous_variant 0.14
rpoB 762114 p.Ile770Val missense_variant 0.14
rpoB 762122 c.2316C>T synonymous_variant 0.14
rpoB 762131 c.2325C>G synonymous_variant 0.12
rpoB 762137 c.2331C>T synonymous_variant 0.12
rpoB 762140 c.2334G>C synonymous_variant 0.12
rpoB 762143 c.2337T>C synonymous_variant 0.12
rpoB 762149 c.2343G>C synonymous_variant 0.15
rpoB 762158 c.2352G>C synonymous_variant 0.15
rpoB 762167 c.2361T>C synonymous_variant 0.15
rpoB 762176 c.2370T>C synonymous_variant 0.15
rpoB 762185 c.2379G>C synonymous_variant 0.15
rpoB 762233 c.2427G>C synonymous_variant 0.23
rpoB 762239 c.2433G>A synonymous_variant 0.23
rpoB 762245 c.2439G>C synonymous_variant 0.24
rpoB 762284 c.2478G>T synonymous_variant 0.25
rpoB 762293 c.2487T>G synonymous_variant 0.27
rpoB 762308 c.2502G>C synonymous_variant 0.2
rpoB 762314 c.2508C>T synonymous_variant 0.2
rpoB 762317 c.2511A>G synonymous_variant 0.2
rpoB 762329 c.2523G>C synonymous_variant 0.19
rpoB 762338 c.2532T>C synonymous_variant 0.12
rpoB 762341 c.2535G>C synonymous_variant 0.12
rpoB 762347 c.2541T>C synonymous_variant 0.13
rpoB 762353 c.2547C>T synonymous_variant 0.13
rpoB 762362 p.Glu852Asp missense_variant 0.13
rpoB 762369 c.2563T>C synonymous_variant 0.15
rpoC 762374 c.-996G>C upstream_gene_variant 0.15
rpoB 762444 p.Ala880Ser missense_variant 0.17
rpoC 763031 c.-339T>C upstream_gene_variant 0.93
rpoC 763621 c.252C>G synonymous_variant 0.11
rpoC 763660 c.291T>G synonymous_variant 0.13
rpoC 763666 c.297G>A synonymous_variant 0.13
rpoC 763675 c.306C>G synonymous_variant 0.13
rpoC 764344 c.975C>T synonymous_variant 0.15
rpoC 764353 c.984G>T synonymous_variant 0.17
rpoC 764365 c.996C>T synonymous_variant 0.16
rpoC 764371 c.1002G>C synonymous_variant 0.16
rpoC 764374 c.1005C>T synonymous_variant 0.16
rpoC 764380 c.1011G>C synonymous_variant 0.16
rpoC 764387 c.1018T>C synonymous_variant 0.17
rpoC 764650 c.1281G>T synonymous_variant 0.15
rpoC 764692 c.1323C>T synonymous_variant 0.24
rpoC 764701 c.1332C>G synonymous_variant 0.26
rpoC 764713 c.1344G>T synonymous_variant 0.26
rpoC 764719 c.1350G>A synonymous_variant 0.27
rpoC 764746 c.1377G>T synonymous_variant 0.19
rpoC 764752 c.1383G>C synonymous_variant 0.18
rpoC 764758 c.1389C>G synonymous_variant 0.21
rpoC 764764 c.1395T>C synonymous_variant 0.2
rpoC 764803 c.1434C>T synonymous_variant 0.24
rpoC 764809 c.1440C>T synonymous_variant 0.24
rpoC 764815 c.1446A>G synonymous_variant 0.23
rpoC 764827 c.1458G>C synonymous_variant 0.18
rpoC 764851 c.1482C>T synonymous_variant 0.17
rpoC 764858 c.1489T>C synonymous_variant 0.17
rpoC 764869 c.1500C>T synonymous_variant 0.17
rpoC 764875 c.1506C>T synonymous_variant 0.17
rpoC 764878 c.1509C>G synonymous_variant 0.14
rpoC 764887 c.1518G>C synonymous_variant 0.12
rpoC 764888 c.1519T>C synonymous_variant 0.12
rpoC 765835 c.2466C>T synonymous_variant 0.12
rpoC 765868 c.2499G>T synonymous_variant 0.12
rpoC 765871 c.2502T>C synonymous_variant 0.12
rpoC 765875 p.Val836Ile missense_variant 0.12
rpoC 765886 c.2517C>G synonymous_variant 0.12
rpoC 765892 c.2523T>C synonymous_variant 0.12
rpoC 765899 c.2530C>T synonymous_variant 0.13
rpoC 765904 c.2535C>G synonymous_variant 0.12
rpoC 766384 c.3015A>G synonymous_variant 0.13
rpoC 766390 c.3021C>T synonymous_variant 0.13
rpoC 766408 c.3039C>T synonymous_variant 0.11
rpoC 766426 c.3057C>T synonymous_variant 0.12
rpoC 766428 c.3059_3060insTAC disruptive_inframe_insertion 0.12
rpoC 766433 c.3065delA frameshift_variant 0.12
rpoC 766442 p.Thr1025Val missense_variant 0.12
rpoC 766456 c.3087C>T synonymous_variant 0.11
rpoC 766539 c.3171_3174delCGGC frameshift_variant 0.12
rpoC 766548 c.3179_3180insACAA frameshift_variant 0.12
rpoC 766573 c.3204T>C synonymous_variant 0.11
rpoC 766579 c.3210C>T synonymous_variant 0.11
rpoC 766582 c.3213C>T synonymous_variant 0.12
rpoC 766585 c.3216T>C synonymous_variant 0.12
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776100 p.Thr794Ile missense_variant 0.9
mmpL5 776182 p.Asp767Asn missense_variant 0.96
mmpL5 779067 c.-587A>G upstream_gene_variant 0.18
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781898 c.339A>C synonymous_variant 0.12
rpsL 781907 c.348T>C synonymous_variant 0.12
rpsL 781916 c.357T>C synonymous_variant 0.14
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0
Rv1258c 1407535 c.-195G>T upstream_gene_variant 0.11
embR 1417116 c.231delT frameshift_variant 0.13
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.15
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.15
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.17
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.16
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.12
rrl 1475602 n.1945G>C non_coding_transcript_exon_variant 0.12
rrl 1475603 n.1946G>C non_coding_transcript_exon_variant 0.12
rrl 1475604 n.1947A>C non_coding_transcript_exon_variant 0.12
rrl 1475612 n.1955G>C non_coding_transcript_exon_variant 0.13
rrl 1475615 n.1958C>G non_coding_transcript_exon_variant 0.13
rrl 1475616 n.1959A>G non_coding_transcript_exon_variant 0.13
rrl 1475637 n.1980T>G non_coding_transcript_exon_variant 0.12
rrl 1475638 n.1981C>G non_coding_transcript_exon_variant 0.12
rrl 1475639 n.1982C>G non_coding_transcript_exon_variant 0.13
rrl 1475643 n.1986C>G non_coding_transcript_exon_variant 0.13
rrl 1475647 n.1990G>C non_coding_transcript_exon_variant 0.13
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.15
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.15
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 1475775 n.2118G>A non_coding_transcript_exon_variant 0.15
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.2
rrl 1475991 n.2334T>C non_coding_transcript_exon_variant 0.18
rrl 1475995 n.2338G>A non_coding_transcript_exon_variant 0.18
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.18
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.2
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.2
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.2
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.21
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.19
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.2
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.2
rrl 1476088 n.2431A>C non_coding_transcript_exon_variant 0.23
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.23
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.23
rrl 1476105 n.2448G>A non_coding_transcript_exon_variant 0.23
rrl 1476106 n.2449A>T non_coding_transcript_exon_variant 0.23
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.29
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.29
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.36
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.31
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.19
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.19
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.21
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.17
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.17
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.17
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.18
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.19
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.19
fabG1 1673597 p.Lys53Thr missense_variant 0.17
fabG1 1673710 p.Leu91Ile missense_variant 0.12
fabG1 1673716 p.Ala93Gln missense_variant 0.12
rpsA 1834177 c.636A>C synonymous_variant 0.96
rpsA 1834411 c.870T>C synonymous_variant 0.12
rpsA 1834423 c.882G>T synonymous_variant 0.13
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918408 p.Phe157Leu missense_variant 0.12
ndh 2102733 p.Leu104Ile missense_variant 0.14
katG 2154724 p.Arg463Leu missense_variant 1.0
PPE35 2167926 p.Leu896Ser missense_variant 1.0
Rv1979c 2223167 c.-3G>T upstream_gene_variant 0.12
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518365 p.Gln84Arg missense_variant 0.11
folC 2746697 p.Asn301Ser missense_variant 0.12
ribD 2986673 c.-166C>T upstream_gene_variant 0.18
ribD 2987487 p.Pro217Thr missense_variant 0.12
Rv2752c 3065876 p.Lys106Glu missense_variant 0.15
thyA 3073970 p.Ala168Pro missense_variant 0.12
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fbiD 3339583 p.Thr156Ala missense_variant 0.17
Rv3083 3449168 p.Ala222Glu missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0
fbiA 3640766 p.Pro75His missense_variant 0.15
rpoA 3878028 c.480G>C synonymous_variant 0.12
ddn 3986987 c.144G>A synonymous_variant 0.12
clpC1 4038721 c.1984C>T synonymous_variant 0.14
clpC1 4038725 c.1980C>G synonymous_variant 0.14
clpC1 4038740 c.1965G>C synonymous_variant 0.12
clpC1 4038755 c.1950G>C synonymous_variant 0.12
clpC1 4038767 c.1938G>C synonymous_variant 0.12
clpC1 4038770 c.1935C>T synonymous_variant 0.13
clpC1 4038773 c.1932T>C synonymous_variant 0.13
clpC1 4038779 c.1926C>G synonymous_variant 0.13
clpC1 4038782 c.1923G>C synonymous_variant 0.13
clpC1 4038790 c.1915C>T synonymous_variant 0.13
clpC1 4038812 c.1893T>C synonymous_variant 0.16
clpC1 4038815 c.1890G>C synonymous_variant 0.17
clpC1 4038842 c.1863G>C synonymous_variant 0.14
clpC1 4038860 c.1845G>C synonymous_variant 0.17
clpC1 4038878 c.1827A>G synonymous_variant 0.2
clpC1 4038890 c.1815G>A synonymous_variant 0.2
clpC1 4038905 c.1800A>G synonymous_variant 0.24
clpC1 4038908 c.1797C>G synonymous_variant 0.24
clpC1 4038911 c.1794G>T synonymous_variant 0.24
clpC1 4038914 c.1791G>C synonymous_variant 0.24
clpC1 4038917 c.1788C>T synonymous_variant 0.24
clpC1 4038923 c.1782A>G synonymous_variant 0.25
clpC1 4038941 c.1764G>C synonymous_variant 0.22
clpC1 4038953 c.1752A>G synonymous_variant 0.15
clpC1 4038956 c.1749T>C synonymous_variant 0.14
clpC1 4038965 c.1740T>C synonymous_variant 0.14
clpC1 4038971 c.1734T>C synonymous_variant 0.12
clpC1 4038989 c.1716T>C synonymous_variant 0.11
clpC1 4039577 c.1128T>C synonymous_variant 0.11
panD 4044146 p.Ile46Val missense_variant 0.17
embC 4239733 c.-130_-129insC upstream_gene_variant 0.12
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4243460 c.228C>T synonymous_variant 1.0
embA 4245026 p.His598Gln missense_variant 0.14
aftB 4267647 p.Asp397Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338710 c.-189A>G upstream_gene_variant 0.12
gid 4407588 c.615A>G synonymous_variant 1.0
gid 4407620 p.Tyr195His missense_variant 1.0
gid 4407783 c.420C>T synonymous_variant 0.15
gid 4407927 p.Glu92Asp missense_variant 1.0
gid 4408430 c.-228G>T upstream_gene_variant 0.17