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	98.5%	213.9 / NA	68	*222* (TAG→TAA)	yieH	phosphoenolpyruvate and 6‑phosphogluconate phosphatase
Reads supporting (aligned to +/- strand):  ref base G (0/0);  major base A (32/35);  minor base T (0/1);  total (32/36)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACGCAGGTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAGTTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGGTGT  >  NC_000913/3897303‑3897573                                                                                                                                         |                                                                                                                                       aCGCAGGTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCTCGTGGTTGGGATATTACGGCATAAtt                                                                                                                                      >  2:60929/1‑139 (MQ=255)   gCAGGTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAAttct                                                                                                                                    >  1:976339/1‑139 (MQ=255)       gTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcac                                                                                                                                <  1:1305370/139‑1 (MQ=255)        tATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGGACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcaca                                                                                                                               >  1:1393120/1‑139 (MQ=255)        tATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcaca                                                                                                                               <  2:936289/139‑1 (MQ=255)             aaGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTccc                                                                                                                          <  2:976339/139‑1 (MQ=255)                 gtTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCGCCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATATTTCGTcac                                                                                                                                <  2:202756/129‑1 (MQ=255)                 gtTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTcac                                                                                                                                >  1:202756/1‑129 (MQ=255)                 gtTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTccc                                                                                                                          <  2:75211/135‑1 (MQ=255)                 gtTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTccc                                                                                                                          >  1:75211/1‑135 (MQ=255)                 gtTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCa                                                                                                                      >  2:1232868/1‑139 (MQ=255)                 gtTCTACTTATGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCa                                                                                                                      >  1:1030289/1‑139 (MQ=255)                                          aaTAAGCCGATCGCTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCa                                                                                             <  2:368323/139‑1 (MQ=255)                                              aGCCGATCTTACACCCGACAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGAGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTAAAAgg                                                                                         <  2:302950/139‑1 (MQ=255)                                                ccGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGGACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgta                                                                                       <  2:1393120/139‑1 (MQ=255)                                                ccGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgta                                                                                       <  2:1030289/139‑1 (MQ=255)                                                    tCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTAcc                                                                                                                >  1:1035505/1‑110 (MQ=255)                                                    tCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTAcc                                                                                                                <  2:1035505/110‑1 (MQ=255)                                                    tCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTAc                                                                                                                 >  1:461077/1‑109 (MQ=255)                                                    tCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTAc                                                                                                                 <  2:461077/109‑1 (MQ=255)                                                    tCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgtaagta                                                                                   >  2:706834/1‑139 (MQ=255)                                                     cGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgtaagtaa                                                                                  <  1:886095/139‑1 (MQ=255)                                                       ttCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAg                                                                                <  1:706834/139‑1 (MQ=255)                                                        tCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAgg                                                                               <  2:1452360/139‑1 (MQ=255)                                                                aaGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGa                                                                       <  1:778795/139‑1 (MQ=255)                                                                aaGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGa                                                                       <  2:784398/139‑1 (MQ=255)                                                                     gtcaccGTGACCCATCTTTCGCAGTTACCTGTACTGTGAAAAGCACGGGGTTGTGATATTACGGCATAATTCGTCACTATCCCTTCACTTACCCTGCTTAAAGTGGTGATCAATGGTAAGTAAAGGGATTTTGATATGt                                                                  <  2:73286/137‑1 (MQ=255)                                                                          cTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGtt                                                             >  1:746373/1‑139 (MQ=255)                                                                             tACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCt                                                                                               <  1:132254/102‑1 (MQ=255)                                                                             tACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCt                                                                                               >  2:132254/1‑102 (MQ=255)                                                                               cccATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCa                                                          >  2:714805/1‑137 (MQ=255)                                                                               cccATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCa                                                          <  1:714805/137‑1 (MQ=255)                                                                               cccATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        <  2:809650/139‑1 (MQ=255)                                                                                    cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAAt                                                                                                      >  2:737392/1‑88 (MQ=255)                                                                                    cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAAt                                                                                                      <  1:737392/88‑1 (MQ=255)                                                                                    cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        <  1:464930/134‑1 (MQ=255)                                                                                    cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCggg                                                   >  2:1518416/1‑139 (MQ=255)                                                                                    cTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTCGATATGTCTGTTTCACg                                                        >  2:464930/1‑134 (MQ=255)                                                                                        cGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGtt                                                                          <  2:1395803/112‑1 (MQ=255)                                                                                        cGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGtt                                                                          >  1:1395803/1‑112 (MQ=255)                                                                                              tACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGgcgc                                                                                                <  1:202126/84‑1 (MQ=255)                                                                                              tACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGgcgc                                                                                                >  2:202126/1‑84 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTccc                                                                                                                          >  1:1488192/1‑47 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTccc                                                                                                                          <  2:1488192/47‑1 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCt                                                                                               >  1:1130761/1‑74 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCt                                                                                               <  2:1130761/74‑1 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGa                                                                       >  2:1362436/1‑98 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGa                                                                       <  1:1362436/98‑1 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTAtt                              >  2:271249/1‑139 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTAtt                              >  2:1337313/1‑139 (MQ=255)                                                                                                         tgGAAAGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTAtt                              >  1:218319/1‑139 (MQ=255)                                                                                                            aaaGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTg                           <  1:271249/139‑1 (MQ=255)                                                                                                             aaGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGc                          <  2:746373/139‑1 (MQ=255)                                                                                                              aGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        >  2:193150/1‑108 (MQ=255)                                                                                                              aGCGCGTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        <  1:193150/108‑1 (MQ=255)                                                                                                                   gTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAg                                                                                >  1:532329/1‑79 (MQ=255)                                                                                                                   gTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAg                                                                                <  2:532329/79‑1 (MQ=255)                                                                                                                   gTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        <  2:1340591/103‑1 (MQ=255)                                                                                                                   gTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACg                                                        >  1:1340591/1‑103 (MQ=255)                                                                                                                   gTGGTTGGGATATTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGtttt                    >  2:670881/1‑139 (MQ=255)                                                                                                                            atatTACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGtt           <  2:218319/139‑1 (MQ=255)                                                                                                                               ttACGGCATAATTCTTCACACTCCCTTCACTTACCCTGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGt                                                                  <  2:1084250/81‑1 (MQ=255)                                                                                                                               ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAggg                                                                              <  2:689112/69‑1 (MQ=255)                                                                                                                               ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAggg                                                                              >  1:689112/1‑69 (MQ=255)                                                                                                                               ttACGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGt                                                                  >  1:1084250/1‑81 (MQ=255)                                                                                                                                 aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgta                                                                                       <  2:1534734/58‑1 (MQ=255)                                                                                                                                 aCGGCATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGgta                                                                                       >  1:1534734/1‑58 (MQ=255)                                                                                                                                     cATAATTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGgtgt  >  1:107582/1‑139 (MQ=255)                                                                                                                                         |                                                                                                                                       ACGCAGGTATGGAAGTGTTCTACTTCTGCGCCGACCCGCACAATAAGCCGATCGTTCACCCGAAAGTCACCACCTTTACCCATCTTTCGCAGTTACCTGAACTGTGGAAAGCGCGTGGTTGGGATATTACGGCATAGTTCTTCACACTCCCTTCACTTACCCCGCTTAAATTGGCGCTCAAAGGTAAGTAAAGGGAGTTTGATATGTCTGTTTCACGTCGGGTAATACATCACGGACTTTATTTTGCAGTTTTAGGACCGTTAATTGGTGT  >  NC_000913/3897303‑3897573

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑