Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	905,720	C→A	17.8%	L270M (CTG→ATG)	amiD →	1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase, Zn‑dependent; OM lipoprotein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	905,720	0	C	A	17.8%	176.1 / 28.1	73	L270M (CTG→ATG)	amiD	1,6‑anhydro‑N‑acetylmuramyl‑L‑alanine amidase, Zn‑dependent; OM lipoprotein
Reads supporting (aligned to +/- strand):  ref base C (24/36);  new base A (6/7);  total (30/43)
Fisher's exact test for biased strand distribution p-value = 7.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.27e-01

AGCAGCGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGTGATGACCGGCTG  >  NC_000913/905622‑905817                                                                                                   |                                                                                                  agcagcGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCt                                                                                                  >  1:176277/1‑100 (MQ=255) agcagcGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCt                                                                                                  <  1:71028/100‑1 (MQ=255)  gcagcGGCGCGTGATTATGACATTCAAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGACGAAGCATTGc                                                                                                   <  2:826715/98‑1 (MQ=255)   cagcGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTgg                                                                                                >  2:230744/1‑100 (MQ=255)   cagcGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTgg                                                                                                <  2:831671/100‑1 (MQ=255)   cagcGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTgg                                                                                                <  2:1307451/100‑1 (MQ=255)   cagcGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTgg                                                                                                <  1:1872965/100‑1 (MQ=255)       ggcgCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGaa                                                                                            <  2:938855/100‑1 (MQ=255)           cgTGATTATGGCATTTCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGgag                                                                                              <  1:2139711/94‑1 (MQ=255)            gTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACg                                                                                       <  1:1051950/100‑1 (MQ=255)             tGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACgg                                                                                      >  2:560497/1‑100 (MQ=255)              gATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACggg                                                                                     <  1:448155/100‑1 (MQ=255)               aTTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTTCTGGAGAAATACGGGc                                                                                    >  1:1786960/1‑100 (MQ=255)               aTTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGc                                                                                    <  2:291528/100‑1 (MQ=255)                 tATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAg                                                                                  <  2:1637368/100‑1 (MQ=255)                 tATGGCATTCCAGATGCATTTCCGCACGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCa                                                                                   <  2:2038491/99‑1 (MQ=255)                  aTGGNATTCCAGATGCANTTCNGCCCGACGTTATATAACGGCGAAGCGGANGCAGAAACTCAGGNGATTGCCNAAGCATNGCTGNAGAAATACGGGCAgg                                                                                 <  2:1350550/100‑1 (MQ=255)                   tGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTAATGGAGAAATACGGGCAGGa                                                                                >  1:4351/1‑100 (MQ=255)                       aTTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAg                                                                            <  2:2190460/100‑1 (MQ=255)                       aTTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGAGGGAGAAATACGGGCAGGATTAg                                                                            <  2:1391008/100‑1 (MQ=255)                        ttCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAgc                                                                           >  1:1798891/1‑100 (MQ=255)                              aTGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCa                                                                     >  2:285624/1‑100 (MQ=255)                               tGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAg                                                                    <  2:560222/100‑1 (MQ=255)                                  aTTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGttt                                                                 >  1:549837/1‑100 (MQ=255)                                   tttCCGCACGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGtttt                                                                >  2:1424819/1‑100 (MQ=255)                                    ttCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTc                                                               >  2:1352400/1‑100 (MQ=255)                                    ttCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTc                                                               <  2:1890047/100‑1 (MQ=255)                                    ttCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTc                                                               <  2:491002/100‑1 (MQ=255)                                     tCCGCCCGACGTTATTTAACGGCGAAGCGGATGCAAAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGGAGGATTAGCGCGGCAGTTTTcc                                                              >  2:1554352/1‑100 (MQ=255)                                       cGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGt                                                            <  2:176274/100‑1 (MQ=255)                                       cGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGt                                                            >  1:1145047/1‑100 (MQ=255)                                              cGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTcgcg                                                     >  1:406171/1‑100 (MQ=255)                                              cGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTcgcg                                                     <  1:2323901/100‑1 (MQ=255)                                               gTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGt                                                    <  1:29820/100‑1 (MQ=255)                                               gTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGt                                                    >  2:3549/1‑100 (MQ=255)                                                ttATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTa                                                   >  2:1889442/1‑100 (MQ=255)                                                 tatataACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAg                                                  >  2:453843/1‑100 (MQ=255)                                                    ataACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGc                                                 >  2:1378147/1‑98 (MQ=255)                                                        cGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAggcg                                           >  1:1328017/1‑100 (MQ=255)                                                        cGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTACCGCGGCAGTTTTCCGTGGTCGCGTAGCCAggcg                                           >  1:873941/1‑100 (MQ=255)                                                        cGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAggcg                                           <  1:2154894/100‑1 (MQ=255)                                                          gCGAAGCGGATGCAGAAACTCATGCGATTGCTGAAGCTTTGCTGGAGGAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAggcggc                                         <  2:1614774/100‑1 (MQ=255)                                                              aGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGtt                                     <  2:1354236/100‑1 (MQ=255)                                                                cGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGtttt                                   <  2:1838760/100‑1 (MQ=255)                                                                   aTGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTtctc                                <  2:492124/100‑1 (MQ=255)                                                                    tGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCg                               <  1:2359898/100‑1 (MQ=255)                                                                    tGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCg                               <  2:2070784/100‑1 (MQ=255)                                                                      cAGAAACTCAGGCGATTGCAGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGAt                             >  2:199031/1‑100 (MQ=255)                                                                        gAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATAc                           <  1:1501673/100‑1 (MQ=255)                                                                         aaaCTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATAcc                          <  1:585472/100‑1 (MQ=255)                                                                             tgtggCGATTGCCGAAGCATGGCTGAAGAAATACGCGCAGGTTTCGGGCGGCAGTTTTCCGTGGTCTCGTAGCCAGGCGGCAGTTTTCTCGATAACTTCa                      <  2:1064618/97‑1 (MQ=255)                                                                             tCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCa                      <  2:818597/100‑1 (MQ=255)                                                                             tCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCACTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCa                      <  2:1328003/100‑1 (MQ=255)                                                                             tCAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCa                      >  1:474976/1‑100 (MQ=255)                                                                              cAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCAt                     >  2:992690/1‑100 (MQ=255)                                                                              cAGGCGATTGCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCAt                     >  2:1504841/1‑100 (MQ=255)                                                                                 ncGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTGCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCa                  >  1:855736/2‑100 (MQ=255)                                                                                 gCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCa                  <  2:886273/100‑1 (MQ=255)                                                                                  cGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAg                 <  1:1839555/100‑1 (MQ=255)                                                                                   gATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAgg                <  2:1546915/100‑1 (MQ=255)                                                                                     ttGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGt              <  1:782544/100‑1 (MQ=255)                                                                                       gCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGtga            <  2:993995/100‑1 (MQ=255)                                                                                       gCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGtga            <  1:2376024/100‑1 (MQ=255)                                                                                       gCCGAAGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGtga            >  1:71621/1‑100 (MQ=255)                                                                                         cGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGtgatg          >  1:2348331/1‑100 (MQ=255)                                                                                         cGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGtgatg          <  2:2053883/100‑1 (MQ=255)                                                                                          gAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGtgatga         <  2:1588418/100‑1 (MQ=255)                                                                                            aGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCTAGGGtgatga         >  2:2160253/1‑98 (MQ=255)                                                                                            aGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGTGATGAcc       >  2:1518601/1‑100 (MQ=255)                                                                                            aGCATTGATGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGTGATGAcc       <  1:417628/100‑1 (MQ=255)                                                                                               aTTGCTGGAGAAATACGAACAGGAATAACGCGTCAGTTTTCCCTGGTCGCGTAGCCAGGCAGCAGTGTTCTCGATCCCTTCATCCAGGGTGATGCCCgg     >  2:1027586/1‑99 (MQ=255)                                                                                                ttGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGTGATGACCGGCt   <  1:624018/100‑1 (MQ=255)                                                                                                 tGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGTGATGACCGGCtn  <  1:328275/100‑2 (MQ=255)                                                                                                 tGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGTGATGACCGGCTg  >  2:1942530/1‑100 (MQ=255)                                                                                                   |                                                                                                  AGCAGCGGCGCGTGATTATGGCATTCCAGATGCATTTCCGCCCGACGTTATATAACGGCGAAGCGGATGCAGAAACTCAGGCGATTGCCGAAGCATTGCTGGAGAAATACGGGCAGGATTAGCGCGGCAGTTTTCCGTGGTCGCGTAGCCAGGCGGCAGTTTTCTCGATACCTTCATCCAGGGTGATGACCGGCTG  >  NC_000913/905622‑905817

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑