Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,456,838	T→C	G154G (GGT→GGC)	gspD →	general secretory pathway component, cryptic

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,456,838	0	T	C	100.0%	231.6 / NA	61	G154G (GGT→GGC)	gspD	general secretory pathway component, cryptic
Reads supporting (aligned to +/- strand):  ref base T (0/0);  new base C (29/32);  total (29/32)

AGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATA  >  NC_000913/3456706‑3456972                                                                                                                                     |                                                                                                                                       aGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgtt                                                                                                                                  <  2:1292841/139‑1 (MQ=255)   ggATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                                <  2:1441703/139‑1 (MQ=255)   ggATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAAtgttgt                                                                                                                                <  1:1198099/139‑1 (MQ=255)         ttGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTa                                                                                                                          >  1:692637/1‑139 (MQ=255)               aCAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAAcc                                                                                                                    >  1:681779/1‑139 (MQ=255)                  gTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTc                                                                                                                 >  2:966276/1‑139 (MQ=255)                  gTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTc                                                                                                                 >  1:499481/1‑139 (MQ=255)                   ttCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTcc                                                                                                                >  1:277104/1‑139 (MQ=255)                    tctcGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCa                                                                                                               >  2:1469148/1‑139 (MQ=255)                     ctcGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  2:681779/139‑1 (MQ=255)                         tCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGtt                                                                                                          <  1:1071426/139‑1 (MQ=255)                                    gTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGAc                                                                                               <  1:144615/139‑1 (MQ=255)                                    gTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGAc                                                                                               <  2:692637/139‑1 (MQ=255)                                        tgaGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGt                                                                                           <  2:277104/139‑1 (MQ=255)                                        tgaGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGt                                                                                           <  2:346332/139‑1 (MQ=255)                                           gTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGt                                                                                        <  1:1187506/139‑1 (MQ=255)                                            ttGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATg                                                                                                                        >  2:599818/1‑106 (MQ=255)                                            ttGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATg                                                                                                                        <  1:599818/106‑1 (MQ=255)                                               gTCACCCGAATTGTACCACTTGAGAACGTTCCTGCTCGTGACCTGGTCCCCCTGCTCCGCCAGATGATGGACGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCt                                                                                    >  2:865186/1‑139 (MQ=255)                                                tCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTc                                                                                   <  1:1049002/139‑1 (MQ=255)                                                    ccGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccacc                                                                               <  1:775129/139‑1 (MQ=255)                                                              ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  2:949130/98‑1 (MQ=255)                                                              ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  1:949130/1‑98 (MQ=255)                                                              ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCt                                                                                    >  1:1176936/1‑124 (MQ=255)                                                              ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCt                                                                                    <  2:1176936/124‑1 (MQ=255)                                                              ccGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAAc                                                                     >  2:596531/1‑139 (MQ=255)                                                                 cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  1:1436452/1‑95 (MQ=255)                                                                 cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  1:1380666/95‑1 (MQ=255)                                                                 cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  2:1436452/95‑1 (MQ=255)                                                                 cTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  2:1380666/1‑95 (MQ=255)                                                                   tGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  1:482188/123‑1 (MQ=255)                                                                   tGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  2:482188/1‑123 (MQ=255)                                                                      gaACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGaa                                                             <  1:596531/139‑1 (MQ=255)                                                                                 cTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAgcg                                                  >  1:393597/1‑139 (MQ=255)                                                                                            gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  2:990708/98‑1 (MQ=255)                                                                                            gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  1:990708/1‑98 (MQ=255)                                                                                            gCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCa                                       <  1:963122/139‑1 (MQ=255)                                                                                               ccccTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCg                                    <  2:393597/139‑1 (MQ=255)                                                                                                       ccGCCAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACagag                            >  1:848577/1‑139 (MQ=255)                                                                                                          ccAGATGATGGATGCGGGTAGCGTCGGCAGTGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGt                                                                                           >  1:1006603/1‑73 (MQ=255)                                                                                                          ccAGATGATGGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCCTATTCTGACCGGt                                                                                           <  2:1006603/73‑1 (MQ=255)                                                                                                              atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              >  2:1405333/1‑50 (MQ=255)                                                                                                              atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCaa                                                                                                              <  1:1405333/50‑1 (MQ=255)                                                                                                              atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  1:746506/80‑1 (MQ=255)                                                                                                              atgatgGATGCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  2:746506/1‑80 (MQ=255)                                                                                                                    gatgCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAatta               <  1:865186/139‑1 (MQ=255)                                                                                                                     atgCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATaaa                                                     >  2:1314580/1‑100 (MQ=255)                                                                                                                     atgCGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATaaa                                                     <  1:1314580/100‑1 (MQ=255)                                                                                                                        cGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                >  1:743438/1‑70 (MQ=255)                                                                                                                        cGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTccac                                                                                <  2:743438/70‑1 (MQ=255)                                                                                                                        cGGGTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCa           >  2:1320029/1‑139 (MQ=255)                                                                                                                          ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATaaa                                                                      >  1:1507816/1‑78 (MQ=255)                                                                                                                          ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATaaa                                                                      <  2:1507816/78‑1 (MQ=255)                                                                                                                          ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               <  2:6980/85‑1 (MQ=255)                                                                                                                          ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               >  1:6980/1‑85 (MQ=255)                                                                                                                          ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               >  2:749648/1‑85 (MQ=255)                                                                                                                          ggTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTg                                                               <  1:749648/85‑1 (MQ=255)                                                                                                                           gTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCgg                                   <  2:700297/112‑1 (MQ=255)                                                                                                                           gTAGCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCgg                                   >  1:700297/1‑112 (MQ=255)                                                                                                                              gCGTCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGa     >  2:922212/1‑139 (MQ=255)                                                                                                                                 tCGGCAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAata  >  1:1209707/1‑139 (MQ=255)                                                                                                                                     |                                                                                                                                       AGGGATGATTGCTGACAGTTCTCGTCCAGGCGTAGGTGATGAGTTGGTCACCCGAATTGTACCGCTTGAGAACGTTCCTGCTCGTGACCTGGCCCCCCTGCTCCGCCAGATGATGGATGCGGGTAGCGTCGGTAATGTTGTGCATTATGAACCCTCCAACGTTCTTATTCTGACCGGTCGTGCCTCCACCATTAATAAACTGATTGAAGTCATAAAGCGCGTTGATGTCATCGGCACAGAGAAGCAGCAAATTATTCATCTGGAATA  >  NC_000913/3456706‑3456972

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑