Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,897,439	G→A	*222* (TAG→TAA)	yieH →	phosphoenolpyruvate and 6‑phosphogluconate phosphatase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,897,439	0	G	A	98.6%	232.0 / NA	73	*222* (TAG→TAA)	yieH	phosphoenolpyruvate and 6‑phosphogluconate phosphatase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (38/34);  minor base T (0/1);  total (38/35)
Fisher's exact test for biased strand distribution p-value = 4.79e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAGTTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGGTGT  >  NC_000913/3897309‑3897573                                                                                                                                   |                                                                                                                                       gTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGTCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcac                                                                                                                                <  2:1038584/139‑1 (MQ=255) gTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcac                                                                                                                                <  2:1012030/139‑1 (MQ=255)  tATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcaca                                                                                                                               <  1:682156/139‑1 (MQ=255)   aTGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCacac                                                                                                                              <  1:499702/139‑1 (MQ=255)           gtTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCa                                                                                                                      >  2:683038/1‑139 (MQ=255)                       cgcCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCtt                                                                                                          >  1:64227/1‑139 (MQ=255)                            aCCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAAtt                                                                                                     >  2:332400/1‑139 (MQ=255)                            aCCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAAtt                                                                                                     >  2:1098331/1‑139 (MQ=255)                                              tCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgtaagta                                                                                   >  1:969214/1‑139 (MQ=255)                                                gTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAgg                                                                                         <  2:1489092/131‑1 (MQ=255)                                                gTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAgg                                                                                         >  1:1489092/1‑131 (MQ=255)                                                gTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTaaa                                                                                 >  1:228808/1‑139 (MQ=255)                                                  tCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTTGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAgg                                                                               >  1:686445/1‑139 (MQ=255)                                                    aCCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcaca                                                                                                                               <  2:992634/89‑1 (MQ=255)                                                    aCCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcaca                                                                                                                               >  1:992634/1‑89 (MQ=255)                                                           aGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGat                                                                      <  1:1098331/139‑1 (MQ=255)                                                                         cccATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        <  1:755474/139‑1 (MQ=255)                                                                           cATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTc                                                      >  2:310336/1‑139 (MQ=255)                                                                           cATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTc                                                      <  1:683038/139‑1 (MQ=255)                                                                             tCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAgg                                                                                         >  2:394380/1‑102 (MQ=255)                                                                             tCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAgg                                                                                         <  1:394380/102‑1 (MQ=255)                                                                              cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTccc                                                                                                                          >  1:305943/1‑68 (MQ=255)                                                                              cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTccc                                                                                                                          <  2:305943/68‑1 (MQ=255)                                                                              cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCa                                                                                             >  2:391141/1‑97 (MQ=255)                                                                              cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCa                                                                                             <  1:391141/97‑1 (MQ=255)                                                                              cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        <  2:180637/134‑1 (MQ=255)                                                                              cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        >  1:180637/1‑134 (MQ=255)                                                                                   gCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTaaa                                                                                                       <  1:514071/82‑1 (MQ=255)                                                                                   gCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTaaa                                                                                                       >  2:514071/1‑82 (MQ=255)                                                                                        tACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCa                                         >  2:1333636/1‑139 (MQ=255)                                                                                              aaCTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcaca                                                                                                                               <  2:1687347/47‑1 (MQ=255)                                                                                              aaCTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcaca                                                                                                                               >  1:1687347/1‑47 (MQ=255)                                                                                                   tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTaaa                                                                                 <  1:351965/88‑1 (MQ=255)                                                                                                   tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTaaa                                                                                 >  2:351965/1‑88 (MQ=255)                                                                                                   tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTAtt                              >  1:1410953/1‑139 (MQ=255)                                                                                                   tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTAtt                              >  2:834317/1‑139 (MQ=255)                                                                                                     gAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTAtttt                            <  1:1333636/139‑1 (MQ=255)                                                                                                     gAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTAtttt                            >  1:340888/1‑139 (MQ=255)                                                                                                       aaGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGc                          <  2:969214/139‑1 (MQ=255)                                                                                                       aaGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGc                          <  2:686445/139‑1 (MQ=255)                                                                                                          cgcgTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCa                                                                                             <  2:647626/69‑1 (MQ=255)                                                                                                          cgcgTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCa                                                                                             >  1:647626/1‑69 (MQ=255)                                                                                                             gTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGtttt                    >  1:1460441/1‑139 (MQ=255)                                                                                                               gtttGGGATATTACGGCACATTTCTTCCCTCTCCCTTCTCTTAGCCCGCTTAAATTGGCGCTCATTAGTAATTATAGGGTGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACTGACTTTATTTTGCAGTTTTAg                  <  2:228808/137‑1 (MQ=255)                                                                                                               ggTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAg                  <  2:340888/139‑1 (MQ=255)                                                                                                                 ttGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGa                <  2:1460441/139‑1 (MQ=255)                                                                                                                     gATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTc                                                                                              <  1:231983/57‑1 (MQ=255)                                                                                                                     gATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTc                                                                                              >  2:231983/1‑57 (MQ=255)                                                                                                                     gATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAgg                                                                                         >  1:1493642/1‑62 (MQ=255)                                                                                                                     gATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAgg                                                                                         <  2:1493642/62‑1 (MQ=255)                                                                                                                         ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGt                                                                  >  2:1614323/1‑81 (MQ=255)                                                                                                                         ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGt                                                                  <  1:1614323/81‑1 (MQ=255)                                                                                                                         ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        >  2:217991/1‑91 (MQ=255)                                                                                                                         ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        <  1:217991/91‑1 (MQ=255)                                                                                                                         ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAAt        <  1:834317/139‑1 (MQ=255)                                                                                                                          tACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAAtt       >  2:1505844/1‑139 (MQ=255)                                                                                                                           aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTgg                                                                                                   >  1:333995/1‑46 (MQ=255)                                                                                                                           aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTgg                                                                                                   <  2:333995/46‑1 (MQ=255)                                                                                                                           aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGat                                                                      >  1:559347/1‑75 (MQ=255)                                                                                                                           aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGat                                                                      <  2:559347/75‑1 (MQ=255)                                                                                                                           aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGa                >  2:1524520/1‑129 (MQ=255)                                                                                                                           aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGa                <  1:1524520/129‑1 (MQ=255)                                                                                                                              gCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgta                                                                                       >  1:1087616/1‑55 (MQ=255)                                                                                                                              gCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgta                                                                                       <  2:1087616/55‑1 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTc                                                                                              >  1:874003/1‑47 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTc                                                                                              <  2:874003/47‑1 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTaaa                                                                                 >  2:319234/1‑60 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTaaa                                                                                 <  1:319234/60‑1 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTACAGGGCGTTTGATATGTCTGTTTCACGTCGGGTAATa                                              >  2:1344632/1‑95 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGgtgt  >  1:1406132/1‑139 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGgtgt  >  1:732840/1‑139 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGgtgt  >  1:267015/1‑139 (MQ=255)                                                                                                                               cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAAGTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATa                                              <  1:1344632/95‑1 (MQ=255)                                                                                                                                   |                                                                                                                                       GTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAGTTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGGTGT  >  NC_000913/3897309‑3897573

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑