Run ID: SRR11972258
Sample name:
Date: 03-04-2023 05:33:51
Number of reads: 371960
Percentage reads mapped: 98.56
Strain: lineage1.1.3
Drug-resistance: HR-TB
Drug | Resistance | Supporting mutations |
---|
Lineage | Family | Main Spoligotype | RDs | Frequency |
---|---|---|---|---|
lineage1 | Indo-Oceanic | EAI | RD239 | 0.95 |
lineage1.1 | Indo-Oceanic | EAI3;EAI4;EAI5;EAI6 | RD239 | 0.92 |
lineage1.1.3 | Indo-Oceanic | EAI6 | RD239 | 0.96 |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs |
---|---|---|---|---|---|
inhA | 1674485 | p.Ile95Thr | missense_variant | 0.5 | isoniazid |
Gene | Chromosome position | Mutation | Type | Estimated fraction |
---|---|---|---|---|
gyrB | 5638 | c.399C>T | synonymous_variant | 1.0 |
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 |
gyrA | 6436 | c.-866C>T | upstream_gene_variant | 1.0 |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 |
gyrA | 7426 | c.127delG | frameshift_variant | 0.17 |
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 |
gyrA | 8452 | p.Ala384Val | missense_variant | 0.96 |
gyrA | 8798 | c.1497C>T | synonymous_variant | 0.15 |
gyrA | 8986 | p.Ser562Tyr | missense_variant | 0.18 |
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.73 |
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 |
mshA | 575907 | p.Ala187Val | missense_variant | 0.38 |
ccsA | 620772 | p.Trp294* | stop_gained | 0.29 |
rpoB | 760223 | c.417T>A | synonymous_variant | 0.2 |
rpoB | 760229 | c.423C>T | synonymous_variant | 0.17 |
rpoB | 761344 | p.Val513Glu | missense_variant | 0.18 |
rpoB | 762063 | p.Ala753Thr | missense_variant | 0.12 |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 |
rpoC | 763561 | c.192G>A | synonymous_variant | 0.29 |
rpoC | 763603 | c.234C>T | synonymous_variant | 0.29 |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.91 |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.86 |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.9 |
rpoC | 765230 | p.Ala621Thr | missense_variant | 1.0 |
rpoC | 766069 | c.2700G>A | synonymous_variant | 0.25 |
rpoC | 766367 | p.Ala1000Thr | missense_variant | 0.17 |
rpoC | 767320 | c.3951G>T | stop_lost&splice_region_variant | 0.29 |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 |
mmpL5 | 775759 | p.Thr908Ala | missense_variant | 0.13 |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 |
mmpL5 | 777572 | c.909C>T | synonymous_variant | 0.78 |
mmpL5 | 777590 | c.891G>A | synonymous_variant | 0.17 |
mmpL5 | 778021 | p.Ala154Pro | missense_variant | 0.22 |
mmpL5 | 778086 | c.394delG | frameshift_variant | 0.18 |
mmpR5 | 778283 | c.-707G>T | upstream_gene_variant | 0.2 |
mmpL5 | 778471 | p.Gln4* | stop_gained | 0.25 |
mmpS5 | 779512 | c.-607C>T | upstream_gene_variant | 0.13 |
mmpS5 | 779645 | c.-740C>A | upstream_gene_variant | 0.12 |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 |
rplC | 800634 | c.-175T>C | upstream_gene_variant | 0.12 |
rplC | 800836 | p.Lys10Glu | missense_variant | 0.12 |
rplC | 800902 | p.Gly32Arg | missense_variant | 0.13 |
rplC | 801327 | p.Asp173Glu | missense_variant | 0.14 |
rplC | 801390 | c.584delA | frameshift_variant | 0.15 |
Rv1258c | 1407435 | c.-95G>A | upstream_gene_variant | 0.29 |
embR | 1416666 | p.Tyr228His | missense_variant | 0.13 |
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 |
fabG1 | 1673367 | c.-72delA | upstream_gene_variant | 0.13 |
rpsA | 1833468 | c.-74T>A | upstream_gene_variant | 0.17 |
rpsA | 1834112 | p.Leu191Met | missense_variant | 0.2 |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.3 |
rpsA | 1834959 | p.Leu473Gln | missense_variant | 0.29 |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 |
tlyA | 1918265 | p.Val109Ala | missense_variant | 0.22 |
ndh | 2101989 | p.Ala352Thr | missense_variant | 0.15 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 |
katG | 2155988 | p.Arg42Trp | missense_variant | 0.22 |
katG | 2156114 | c.-3G>T | upstream_gene_variant | 0.15 |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 |
PPE35 | 2167983 | p.Gly877Asp | missense_variant | 0.71 |
PPE35 | 2169029 | p.Asp528Asn | missense_variant | 0.29 |
PPE35 | 2169041 | c.1572G>A | synonymous_variant | 0.5 |
PPE35 | 2169044 | c.1569G>C | synonymous_variant | 0.3 |
PPE35 | 2169047 | p.Ile522Val | missense_variant | 0.3 |
PPE35 | 2169053 | c.1560T>C | synonymous_variant | 0.8 |
PPE35 | 2169056 | c.1557A>G | synonymous_variant | 0.3 |
PPE35 | 2169059 | c.1554G>A | synonymous_variant | 0.5 |
PPE35 | 2169063 | p.Met517Thr | missense_variant | 0.8 |
PPE35 | 2169065 | p.Ala516Ile | missense_variant | 0.5 |
PPE35 | 2169068 | c.1545G>T | synonymous_variant | 0.5 |
PPE35 | 2169071 | c.1542A>G | synonymous_variant | 0.23 |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 |
pncA | 2289183 | p.Ala20Val | missense_variant | 0.2 |
pncA | 2290099 | c.-858C>T | upstream_gene_variant | 0.25 |
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 |
eis | 2714808 | p.Phe175Leu | missense_variant | 0.22 |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.88 |
folC | 2746438 | c.1161G>A | synonymous_variant | 0.22 |
folC | 2746874 | p.Met242Thr | missense_variant | 0.22 |
folC | 2747544 | p.Pro19Ser | missense_variant | 0.4 |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 1.0 |
Rv2752c | 3065735 | p.Ala153Thr | missense_variant | 0.4 |
Rv2752c | 3065783 | p.Gly137Ser | missense_variant | 0.29 |
thyX | 3067222 | p.Ala242Thr | missense_variant | 0.17 |
thyX | 3068144 | c.-199T>A | upstream_gene_variant | 0.18 |
thyA | 3074395 | p.Thr26Ile | missense_variant | 0.17 |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 |
ald | 3087085 | p.Gln89Arg | missense_variant | 0.15 |
ald | 3087572 | c.753G>A | synonymous_variant | 0.18 |
Rv3083 | 3448514 | c.14delT | frameshift_variant | 0.18 |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 |
Rv3083 | 3449496 | c.993C>T | synonymous_variant | 0.17 |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 |
fprA | 3474014 | p.Pro3Leu | missense_variant | 0.57 |
fprA | 3474597 | c.591C>A | synonymous_variant | 1.0 |
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 |
fbiB | 3641719 | p.Pro62Leu | missense_variant | 0.2 |
fbiB | 3642156 | p.Lys208Glu | missense_variant | 0.25 |
fbiB | 3642700 | p.Ala389Val | missense_variant | 0.25 |
alr | 3840689 | c.732C>T | synonymous_variant | 1.0 |
alr | 3841253 | c.168C>T | synonymous_variant | 0.94 |
alr | 3841277 | c.144C>T | synonymous_variant | 0.94 |
rpoA | 3878027 | c.480delG | frameshift_variant | 0.15 |
clpC1 | 4038397 | p.Ala770Ser | missense_variant | 0.12 |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.91 |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.75 |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.8 |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 |
embA | 4243848 | p.Val206Met | missense_variant | 0.92 |
embA | 4244360 | c.1128C>T | synonymous_variant | 0.15 |
embA | 4244875 | p.Pro548Arg | missense_variant | 0.22 |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.91 |
embB | 4247223 | p.Trp237* | stop_gained | 0.2 |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.67 |
aftB | 4267768 | c.1069C>T | synonymous_variant | 0.14 |
ubiA | 4268959 | p.Ile292Lys | missense_variant | 0.5 |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 |
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.7 |
ethR | 4327362 | c.-187G>T | upstream_gene_variant | 0.14 |
ethR | 4327820 | p.Ala91Val | missense_variant | 0.18 |
ethA | 4328148 | c.-675C>T | upstream_gene_variant | 0.29 |
ethA | 4328222 | c.-749G>A | upstream_gene_variant | 0.22 |
ethA | 4328251 | c.-778G>A | upstream_gene_variant | 0.18 |
ethA | 4328287 | c.-814G>T | upstream_gene_variant | 0.18 |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 |
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 |
gid | 4407780 | c.423G>A | synonymous_variant | 1.0 |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 |