Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,459,354	T→C	V339A (GTA→GCA)	gspE →	general secretory pathway component, cryptic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,459,354	0	T	C	100.0%	233.5 / NA	60	V339A (GTA→GCA)	gspE	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (27/33);  total (27/33)

GTGTGGATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTT  >  NC_000913/3459222‑3459472                                                                                                                                     |                                                                                                                       gtgtGGATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACtctc                                                                                                                  >  1:1029272/1‑139 (MQ=255)  tgtgGATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCAGCCATCTGGCACTCTCa                                                                                                                 <  2:238567/139‑1 (MQ=255)      gATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCaa                                                                                                                <  2:185582/136‑1 (MQ=255)      gATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCaa                                                                                                                >  1:185582/1‑136 (MQ=255)      gATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAacac                                                                                                             <  2:362427/139‑1 (MQ=255)      gATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAacac                                                                                                             <  1:1331257/139‑1 (MQ=255)        tatGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTc                                                                                                           <  1:1261379/139‑1 (MQ=255)        tatGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTc                                                                                                           <  2:1120753/139‑1 (MQ=255)          tGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCca                                                                                                         >  1:1239736/1‑139 (MQ=255)           gTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAacac                                                                                                             >  2:167616/1‑134 (MQ=255)           gTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAacac                                                                                                             <  1:167616/134‑1 (MQ=255)           gTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCcac                                                                                                        >  2:958143/1‑139 (MQ=255)           gTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCcac                                                                                                        >  2:280104/1‑139 (MQ=255)            tCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATCGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCcaca                                                                                                       >  2:937342/1‑139 (MQ=255)              tttCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACt                                                                                                     <  2:852862/139‑1 (MQ=255)               ttCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTa                                                                                                    >  2:1059329/1‑139 (MQ=255)                tcgctcgcGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTaa                                                                                                   >  2:1203877/1‑139 (MQ=255)                       cgGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCa                                                                                            >  1:335886/1‑139 (MQ=255)                       cgGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCa                                                                                            >  1:1268528/1‑139 (MQ=255)                                       cTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGAccc                                                                            <  1:1412002/139‑1 (MQ=255)                                                gACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCcgcg                                                                   >  2:612118/1‑139 (MQ=255)                                                     ggATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATg                                                              <  1:280104/139‑1 (MQ=255)                                                     ggATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATg                                                              <  1:958143/139‑1 (MQ=255)                                                         gtcgtcATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCg                                                          <  2:1291223/139‑1 (MQ=255)                                                         gtcgtcATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCg                                                          <  2:1029272/139‑1 (MQ=255)                                                         gtcgtcATAGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCg                                                          <  1:937342/139‑1 (MQ=255)                                                          tcgtcATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGt                                                         <  2:812159/139‑1 (MQ=255)                                                            gtcATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCcac                                                                                                        >  1:962783/1‑90 (MQ=255)                                                            gtcATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCcac                                                                                                        <  2:962783/90‑1 (MQ=255)                                                             tcATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGa                                                      <  2:211436/139‑1 (MQ=255)                                                                tggtggGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATc                                                   >  2:266024/1‑139 (MQ=255)                                                                 ggtggGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCa                                                  >  2:1150805/1‑139 (MQ=255)                                                                     ggggAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTcc                                              >  2:1291973/1‑139 (MQ=255)                                                                         aaaTTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCt                                          <  2:1047127/139‑1 (MQ=255)                                                                             tCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACa                                                                >  2:71745/1‑113 (MQ=255)                                                                             tCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACa                                                                <  1:71745/113‑1 (MQ=255)                                                                               gTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTc                                    <  1:1358419/139‑1 (MQ=255)                                                                                      aGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTg                             <  2:335886/139‑1 (MQ=255)                                                                                      aGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTg                             <  2:1268528/139‑1 (MQ=255)                                                                                             gcgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTc                                                                                                           <  1:1174804/54‑1 (MQ=255)                                                                                             gcgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTc                                                                                                           >  2:1174804/1‑54 (MQ=255)                                                                                             gcgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAg                                                                                        >  1:363487/1‑73 (MQ=255)                                                                                             gcgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAg                                                                                        <  2:363487/73‑1 (MQ=255)                                                                                              cgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTc                                                                                                           <  1:1193678/53‑1 (MQ=255)                                                                                              cgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTc                                                                                                           >  2:1193678/1‑53 (MQ=255)                                                                                              cgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTc                                    >  1:455803/1‑124 (MQ=255)                                                                                              cgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTc                                    <  2:455803/124‑1 (MQ=255)                                                                                              cgcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGAt                     >  2:84179/1‑139 (MQ=255)                                                                                               gcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCg                                                          >  2:875260/1‑101 (MQ=255)                                                                                               gcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCg                                                          <  1:875260/101‑1 (MQ=255)                                                                                               gcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCAt                                                 >  2:47741/1‑110 (MQ=255)                                                                                               gcAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCAt                                                 <  1:47741/110‑1 (MQ=255)                                                                                                           tCAGGCCTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGt        <  1:1173707/139‑1 (MQ=255)                                                                                                                 cTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCg                                                       >  1:1237342/1‑86 (MQ=255)                                                                                                                 cTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCg                                                       <  2:1237342/86‑1 (MQ=255)                                                                                                                 cTCGCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGtt  <  1:1291973/139‑1 (MQ=255)                                                                                                                    gCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCAt                                                 >  2:789840/1‑89 (MQ=255)                                                                                                                    gCTCACCGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCAt                                                 <  1:789840/89‑1 (MQ=255)                                                                                                                         ccGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGt                                     >  2:1121963/1‑96 (MQ=255)                                                                                                                         ccGGCCATCTGGCACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGt                                     <  1:1121963/96‑1 (MQ=255)                                                                                                                                     |                                                                                                                       GTGTGGATATGTCTTTCGCTCGCGGCCTGCGCGCCATACTTCGCCAGGACCCGGATGTCGTCATGGTGGGGGAAATTCGTGATACAGAAACCGCGCAGATTGCGGTTCAGGCCTCGCTCACCGGCCATCTGGTACTCTCAACACTCCACACTAACAGTGCATCAGGCGCAGTGACCCGGCTCCGCGACATGGGCGTCGAATCATTCCTGCTTTCGTCTTCCCTGGCAGGGATTATCGCGCAACGTCTGGTT  >  NC_000913/3459222‑3459472

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑