Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,465,441	G→A	T120T (ACG→ACA)	gspM →	general secretory pathway component, cryptic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,465,441	0	G	A	100.0%	239.1 / NA	74	T120T (ACG→ACA)	gspM	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base G (0/0);  new base A (30/44);  total (30/44)

AGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACAATAATGACAATGCTACTGCC  >  NC_000913/3465305‑3465559                                                                                                                                         |                                                                                                                       aGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGc                                                                                                                      <  1:304158/139‑1 (MQ=255)  gCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGca                                                                                                                     <  1:151529/139‑1 (MQ=255)      aTCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAgg                                                                                                                 <  2:875567/139‑1 (MQ=255)        cAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTa                                                                                                               <  2:542294/139‑1 (MQ=255)             atatCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          <  2:836535/139‑1 (MQ=255)             atatCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          >  2:784944/1‑139 (MQ=255)             atatCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          <  2:49749/139‑1 (MQ=255)                   ttCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTAt                                                                                                    <  1:477196/139‑1 (MQ=255)                   ttCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTAt                                                                                                    <  1:1091540/139‑1 (MQ=255)                    tctcGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGcac                                                                                                                    >  2:1491564/1‑122 (MQ=255)                    tctcGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGcac                                                                                                                    <  1:1491564/122‑1 (MQ=255)                     ctcGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          <  2:354458/131‑1 (MQ=255)                     ctcGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          >  1:354458/1‑131 (MQ=255)                      tcGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGt                                                                                                 >  1:548257/1‑139 (MQ=255)                                aaaaCGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGAc                                                                                       <  1:86034/139‑1 (MQ=255)                                   aCGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCtt                                                                                    <  2:1461153/139‑1 (MQ=255)                                         gaATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGttt                                                                              <  2:1011802/139‑1 (MQ=255)                                            tttGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTAct                                                                           >  1:627374/1‑139 (MQ=255)                                                          tGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGa                                                             <  1:1005886/139‑1 (MQ=255)                                                                aCGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGAt                                                       <  2:657394/139‑1 (MQ=255)                                                                    cccGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTa                                                                                                               >  1:1028292/1‑79 (MQ=255)                                                                    cccGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTa                                                                                                               <  2:1028292/79‑1 (MQ=255)                                                                                tctGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTg                                       >  2:1355278/1‑139 (MQ=255)                                                                                 ctGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          <  2:829994/71‑1 (MQ=255)                                                                                 ctGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          >  1:829994/1‑71 (MQ=255)                                                                                  tGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGcac                                                                                                                    >  1:338925/1‑60 (MQ=255)                                                                                  tGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGcac                                                                                                                    <  2:338925/60‑1 (MQ=255)                                                                                  tGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACg                                                              <  1:623884/114‑1 (MQ=255)                                                                                  tGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACg                                                              >  2:623884/1‑114 (MQ=255)                                                                                  tGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTc                                     >  2:150930/1‑139 (MQ=255)                                                                                       aTTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          >  1:327674/1‑65 (MQ=255)                                                                                       aTTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          <  2:640210/65‑1 (MQ=255)                                                                                       aTTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          <  2:327674/65‑1 (MQ=255)                                                                                       aTTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATa                                                                                                          >  1:640210/1‑65 (MQ=255)                                                                                       aTTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGTTCACCCTCAGGCATTTGTCCTTCa                                >  2:750467/1‑139 (MQ=255)                                                                                       aTTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCa                                <  1:1355278/139‑1 (MQ=255)                                                                                       aTTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCa                                <  2:216946/139‑1 (MQ=255)                                                                                          cATCCTGTCACCGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGTTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAggg                             <  1:90450/139‑1 (MQ=255)                                                                                             ccTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGc                          <  2:548257/139‑1 (MQ=255)                                                                                              cTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGca                         <  2:627374/139‑1 (MQ=255)                                                                                              cTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGca                         >  2:578691/1‑139 (MQ=255)                                                                                               tGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGTTCACCCTCAGGCATTTGTCCTTCAGGGAGcaa                        <  1:750467/139‑1 (MQ=255)                                                                                                gTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGa                                                                  <  2:896625/96‑1 (MQ=255)                                                                                                gTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGa                                                                  >  1:896625/1‑96 (MQ=255)                                                                                                   acaGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACaat                    >  2:1427897/1‑139 (MQ=255)                                                                                                      gCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACaataat                 <  1:150930/139‑1 (MQ=255)                                                                                                      gCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACaataat                 <  1:784944/139‑1 (MQ=255)                                                                                                      gCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACaataat                 <  1:605437/139‑1 (MQ=255)                                                                                                       ttCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGAcc                                                                                      <  2:391973/68‑1 (MQ=255)                                                                                                       cTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTAt                                                                                                    <  2:135265/55‑1 (MQ=255)                                                                                                       cTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTAt                                                                                                    >  1:135265/1‑55 (MQ=255)                                                                                                       cTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGAcc                                                                                      >  1:391973/1‑69 (MQ=255)                                                                                                       cTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCAccc                                                  >  1:509682/1‑105 (MQ=255)                                                                                                       cTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCAccc                                                  <  2:509682/105‑1 (MQ=255)                                                                                                       cTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACAATAATg                >  1:149576/1‑139 (MQ=255)                                                                                                         ccccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGt                                                                                                                <  1:1103151/41‑1 (MQ=255)                                                                                                         ccccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGt                                                                                                                >  2:1103151/1‑41 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGc                                                                      >  2:1149110/1‑81 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGc                                                                      <  1:1149110/81‑1 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCAccc                                                  <  1:743/101‑1 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCAccc                                                  >  2:743/1‑101 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGc                                            >  1:1476450/1‑107 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGc                                            <  2:1476450/107‑1 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGca                         >  2:1159223/1‑126 (MQ=255)                                                                                                           ccTCGAAAACGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGca                         <  1:1159223/126‑1 (MQ=255)                                                                                                               gAAAACGTCTCCCGCTGGCTCACTACAGCACAGGt                                                                                                                <  2:1492785/35‑1 (MQ=255)                                                                                                               gAAAACGTCTCCCGCTGGCTCACTACAGCACAGGt                                                                                                                >  1:1492785/1‑35 (MQ=255)                                                                                                                    cGTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACAATAATGAc              <  1:878026/128‑1 (MQ=255)                                                                                                                    cGTCTCCCGCTGGCTCAATACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACAATAATGAc              >  2:878026/1‑128 (MQ=255)                                                                                                                     gTCTCCCGCTGGCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACAATAATGACAATGCTACTGcc  <  2:1061746/139‑1 (MQ=255)                                                                                                                                gCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTAct                                                                           <  1:1518223/55‑1 (MQ=255)                                                                                                                                gCTCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTAct                                                                           >  2:1518223/1‑55 (MQ=255)                                                                                                                                  tCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGAt                                                       >  2:113654/1‑73 (MQ=255)                                                                                                                                  tCACTACAGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGAt                                                       <  1:113654/73‑1 (MQ=255)                                                                                                                                         |                                                                                                                       AGCCCATCAAAAATATCCTTCTCGAGGAAGCAAAACGTGAGAATTTGGCTATCACGCTGGAAAACGGCCCGGACAATACTCTGACAATTCATCCTGTCACAGCTCCCCTCGAAAACGTCTCCCGCTGGCTCACTACGGCACAGGTAACATACGGTATTGTTATTGAAGACCTTCAGTTTACTCTTGCCGGAAACGAAGAGATCACCCTCAGGCATTTGTCCTTCAGGGAGCAACAATAATGACAATGCTACTGCC  >  NC_000913/3465305‑3465559

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑