Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913_3_pae_tpiA	4,296,297	+GC	intergenic (+587/+55)	gltP → / ← yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913_3_pae_tpiA	4,296,296	1	.	C	93.8%	124.3 / 2.3	50	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/3);  new base C (16/29);  total (17/33)
Fisher's exact test for biased strand distribution p-value = 5.41e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01
*	NC_000913_3_pae_tpiA	4,296,296	2	.	G	94.0%	141.1 / 2.4	50	intergenic (+586/+56)	gltP/yjcO	glutamate/aspartate:proton symporter/Sel1 family TPR‑like repeat protein
Reads supporting (aligned to +/- strand):  ref base . (0/3);  new base G (17/30);  total (17/33)
Fisher's exact test for biased strand distribution p-value = 5.42e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.97e-01

GACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑A‑‑C‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGCG  >  NC_000913_3_pae_tpiA/4296212‑4296431                                                                                         ||                                                                                                                                          gACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATTCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCg                                                                           >  2:982887/1‑149 (MQ=255) gACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCg                                                                           >  2:605852/1‑149 (MQ=12)    gCTTAAAGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTg                                                                        >  2:444637/1‑149 (MQ=255)      tgaaCGCGTTTTCTCAGGCTTACGCTAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGt                                                                      <  2:294630/147‑1 (MQ=11)         aCGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGCTTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGttga                                                                   >  1:426274/1‑147 (MQ=11)               tttATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                             <  1:985678/148‑1 (MQ=255)               cTTATCAGGCCTACGGCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                             <  1:632319/149‑1 (MQ=255)               cTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTc                                                             >  1:1004540/1‑149 (MQ=255)                ttATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCa                                                            <  1:81205/149‑1 (MQ=255)                gtATCAGGGCTACGCCAGACAGCGCAAGAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCa                                                            <  2:223129/148‑1 (MQ=14)                  aTCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCaaa                                                          <  1:677737/149‑1 (MQ=255)                     aGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAActc                                                       >  1:907197/1‑149 (MQ=255)                        ccgaCGCCAGACAGCGCAGTGGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTc                                                    <  2:783109/146‑1 (MQ=17)                         cTACACCAGACAGTGCCATAGCCTGATTTAGCGTTATTTTGTAGGTCCGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAAGGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTGACCGTTGGTTAATTTTTCAAACTCTTca                                                   <  1:1006343/149‑1 (MQ=14)                            cGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCacac                                                <  1:605852/149‑1 (MQ=255)                              ccAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGAAATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACAccc                                              >  2:785803/1‑149 (MQ=255)                                aGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCgg                                            >  2:998706/1‑149 (MQ=255)                                    agagcAATAGCATGACTGAGCGTGATTTTGTGGGTCGGATAAGGCGT‑TTCCG‑‑C‑C‑GCATGCGACATCAATGCCTGATGCGACGCTTGCCGCCTCTTATTAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATc                                        <  2:174692/146‑1 (MQ=18)                                       gcAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑A‑‑CGCAGCATCATGCATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCaaa                                     <  1:770926/149‑1 (MQ=18)                                        cAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAAc                                    >  1:256360/1‑149 (MQ=255)                                         aaTAGCCGGATTGAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑ACATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGAATCAAAcc                                   <  2:179268/149‑1 (MQ=18)                                          aTAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAAccc                                  <  2:686799/149‑1 (MQ=255)                                             gCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTc                               <  1:444637/149‑1 (MQ=255)                                              ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTcc                              >  1:68519/1‑149 (MQ=255)                                              ccTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTcc                              <  1:150702/149‑1 (MQ=255)                                              ccTGATTTAGCGTGATTCTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTcc                              <  1:878262/149‑1 (MQ=255)                                               cTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCa                             <  1:150550/149‑1 (MQ=255)                                               cTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCa                             <  1:838317/149‑1 (MQ=255)                                               cTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCAACCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCa                             >  2:768449/1‑149 (MQ=255)                                                 gATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa                           <  2:335351/149‑1 (MQ=255)                                                 gATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATa                           <  2:185286/149‑1 (MQ=255)                                                  aTTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ATGC‑C‑GCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATAc                          >  2:577325/1‑149 (MQ=255)                                                   tttAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ATGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACa                         <  2:329999/149‑1 (MQ=255)                                                    ttAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAg                        <  2:703944/149‑1 (MQ=255)                                                    ttAGCGTGATGTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAg                        <  1:715312/149‑1 (MQ=255)                                                         gTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAg                   <  1:642955/149‑1 (MQ=255)                                                         gTGATTTTGTAGGGCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAg                   <  1:327656/149‑1 (MQ=255)                                                          tGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAgg                  <  2:147952/149‑1 (MQ=255)                                                          tGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATGTTAACCGTTGGTTAAttt                                                                >  1:397358/1‑103 (MQ=11)                                                          tGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAACGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAAttt                                                                <  2:397358/103‑1 (MQ=11)                                                           gATTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGt                 <  1:280078/149‑1 (MQ=255)                                                           gATTTTGTAGGTCGCATAAGGAGTATTC‑G‑‑C‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGt                 <  1:765741/149‑1 (MQ=25)                                                            aTTTTGTAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGtt                <  2:242309/149‑1 (MQ=255)                                                                  tAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTCACCGTTGGTTAATTTTTCAAACTTTTCATTCTCGGTATCAAACCCTTCCATACAGCTCAGGTTCAATCa          >  1:899684/1‑149 (MQ=21)                                                                  tAGGTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGCATCAAACCCTTCCATACAGCTCAGCTTCAACCa          >  1:128902/1‑149 (MQ=25)                                                                    ggTCGGATAAGGCGT‑CT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGt        <  2:300247/149‑1 (MQ=255)                                                                     gTCGGATAAGGGGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCCTTCAGCTTAGGTTTACCCAATg       >  1:171333/1‑149 (MQ=21)                                                                     gTCGGATAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATTGGAGGCTTGCCGCGTCTTATCAGGCCTCTCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCACACCCTTCCATACATCTCCGGTTCAACCAGTg       >  2:173581/1‑149 (MQ=25)                                                                       cGGATCCGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCa     <  1:418294/149‑1 (MQ=37)                                                                          aTAAGGCGT‑TT‑‑ACGC‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAgcg  <  2:156378/149‑1 (MQ=255)                                                                                         ||                                                                                                                                          GACGCTTAACGCGTCTTATCAGGCCTACGCCAGACAGCGCAATAGCCTGATTTAGCGTGATTTTGTAGGTCGGATAAGGCGT‑TT‑‑A‑‑C‑C‑GCATCCGACATCAATGCCTGATGCGACGCTTGCCGCGTCTTATCAGGCCTATCTTAACCGTTGGTTAATTTTTCAAACTCTTCACACCCGGTATCAAACCCTTCCATACAGCTCAGGTTCAACCAGTGCAGCG  >  NC_000913_3_pae_tpiA/4296212‑4296431

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑