Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,031,761	T→C	intergenic (‑49/‑378)	serT ← / → hyaA	tRNA‑Ser/hydrogenase 1, small subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,031,761	0	T	C	97.1%	234.7 / ‑1.9	69	intergenic (‑49/‑378)	serT/hyaA	tRNA‑Ser/hydrogenase 1, small subunit
Reads supporting (aligned to +/- strand):  ref base T (1/1);  new base C (27/39);  total (29/40)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.73e-01

CGCCGGTTTTCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAATTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCTTTTACT  >  NC_000913/1031667‑1031857                                                                                               |                                                                                                 cGCCGGTTTTCAAGACCGTTGCCTTCAACCGCTCGGCCACACTTCCGGAATCACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAActtgtt                                                                                             <  2:1174747/100‑1 (MQ=255) cGCCGGTTTTCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAActtgtt                                                                                             >  2:1176500/1‑100 (MQ=255)  gCCGGTTTTCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAActtgttt                                                                                            <  1:529082/100‑1 (MQ=255)    cGGTTTTCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAActtgtttgt                                                                                          <  1:754313/100‑1 (MQ=255)    cGGTTTTCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAActtgtttgt                                                                                          >  1:313811/1‑100 (MQ=255)       ttttCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAActtgtttgtttg                                                                                       <  2:694315/100‑1 (MQ=255)       ttttCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAActtgtttgtttg                                                                                       >  2:161102/1‑100 (MQ=255)         ttCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGcc                                                                                     <  2:134279/100‑1 (MQ=255)          tCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCt                                                                                    >  1:1105615/1‑100 (MQ=255)          tCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCt                                                                                    >  2:1496756/1‑100 (MQ=255)          tCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCt                                                                                    >  1:1485573/1‑100 (MQ=255)           cAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAGTGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTg                                                                                   >  2:965944/1‑100 (MQ=255)           cAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAACCATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTg                                                                                   >  2:1357010/1‑100 (MQ=255)           cAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTg                                                                                   >  2:903058/1‑100 (MQ=255)           cAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTg                                                                                   >  2:1356991/1‑100 (MQ=255)            aaGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGa                                                                                  >  1:207510/1‑100 (MQ=255)             aGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAATTTGTTTGTTTGCCTGaa                                                                                 <  1:895398/100‑1 (MQ=255)             aGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGaa                                                                                 >  2:1129076/1‑100 (MQ=255)             aGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGaa                                                                                 >  1:737764/1‑100 (MQ=255)             aGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGaa                                                                                 >  1:54314/1‑100 (MQ=255)              gACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAATTTGTTTGTTTGCCTGaaa                                                                                >  1:904984/1‑100 (MQ=255)              gACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGaaa                                                                                <  1:1994/100‑1 (MQ=255)               aCCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGaaaa                                                                               <  2:1488697/100‑1 (MQ=255)                  ggTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACa                                                                            <  1:1395747/100‑1 (MQ=255)                  ggTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACa                                                                            >  2:147721/1‑100 (MQ=255)                  ggTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACa                                                                            >  1:277283/1‑100 (MQ=255)                   gTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAg                                                                           <  2:1016916/100‑1 (MQ=255)                    tGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGc                                                                          >  2:507230/1‑100 (MQ=255)                      ccTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCa                                                                        <  1:369252/100‑1 (MQ=255)                          cAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAg                                                                    <  2:1149737/100‑1 (MQ=255)                            aCCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTg                                                                  <  2:272652/100‑1 (MQ=255)                            aCCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAAATTGTTTGTTTGCCTGAAAAACAGCCAAAAGTg                                                                  >  2:1105672/1‑100 (MQ=255)                              cGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCa                                                                >  1:294359/1‑100 (MQ=255)                               gCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCAt                                                               <  1:58754/100‑1 (MQ=255)                                 tCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTg                                                             <  2:1141509/100‑1 (MQ=255)                                    gCCACACTTCCGGAATGACGCGCACTATAAAGATCCCGATGCGGCGTCTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATa                                                          <  2:1060848/100‑1 (MQ=255)                                      cacaCTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGc                                                        >  1:86194/1‑100 (MQ=255)                                         acTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGCAAAACAGCCAAAAGTGCATTGATAGCGTg                                                     >  2:52247/1‑100 (MQ=255)                                         acTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTg                                                     <  2:207509/100‑1 (MQ=255)                                         acTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTg                                                     <  2:165993/100‑1 (MQ=255)                                            tCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGaaa                                                  <  2:867602/100‑1 (MQ=255)                                             ccGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGAGCATTGATAGCGTGAAAt                                                 >  2:488784/1‑100 (MQ=255)                                                 aaTGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAAca                                             <  1:965952/100‑1 (MQ=255)                                                  aTGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAAcag                                            <  1:487321/100‑1 (MQ=255)                                                  aTGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAAcag                                            <  2:530850/100‑1 (MQ=255)                                                          cACTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGa                                    >  2:922820/1‑100 (MQ=255)                                                           aCTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGAt                                   <  2:875618/100‑1 (MQ=255)                                                            cTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATc                                  <  1:1381959/100‑1 (MQ=255)                                                            cTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATc                                  <  1:641906/100‑1 (MQ=255)                                                            cTATAAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATc                                  <  1:484640/100‑1 (MQ=255)                                                             tataAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCa                                 <  1:1385054/100‑1 (MQ=255)                                                              ataAACATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCAt                                >  2:1061190/1‑100 (MQ=255)                                                                aaaCATCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCAttt                              <  1:901058/100‑1 (MQ=255)                                                                     tCCCGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTtcatca                         <  2:54314/100‑1 (MQ=255)                                                                      cccGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCAc                        <  2:48127/100‑1 (MQ=255)                                                                        cGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCa                      <  1:256009/100‑1 (MQ=255)                                                                        cGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCa                      <  2:235913/100‑1 (MQ=255)                                                                        cGATGCGGCGTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCa                      <  1:488787/100‑1 (MQ=255)                                                                        cGATGCGGCGTGTAAACCCCTAACTTGTTGGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCa                      <  2:1183645/100‑1 (MQ=255)                                                                            gcggcgTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGaa                  <  2:12308/100‑1 (MQ=255)                                                                                cgTGTAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTcc              >  2:320266/1‑100 (MQ=255)                                                                                 gtgtAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCt             >  2:468633/1‑100 (MQ=255)                                                                                   gtAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTtc           <  2:542118/100‑1 (MQ=255)                                                                                    tAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTtct          >  2:1027000/1‑100 (MQ=255)                                                                                    tAAACCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTtct          <  1:807037/100‑1 (MQ=255)                                                                                     aaaCCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTtctc         <  1:1161592/100‑1 (MQ=255)                                                                                     aaaCCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTtctc         <  1:691501/100‑1 (MQ=255)                                                                                      aaCCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTctct        >  2:1198000/1‑100 (MQ=255)                                                                                       aCCCCTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCtt       <  2:277282/100‑1 (MQ=255)                                                                                        ccccTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCttt      <  2:1485563/100‑1 (MQ=255)                                                                                        ccccTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCttt      >  2:1458841/1‑100 (MQ=255)                                                                                        ccccTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCttt      >  1:941365/1‑100 (MQ=255)                                                                                         cccTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCtttt     >  2:391825/1‑100 (MQ=255)                                                                                         cccTAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCtttt     <  2:977547/100‑1 (MQ=255)                                                                                            tAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCTTTTACt  <  1:836985/100‑1 (MQ=255)                                                                                            tAACTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTAATCATTTCATCACCATGAATTCCTTCTCTTTTACt  <  1:837441/100‑1 (MQ=255)                                                                                               |                                                                                                 CGCCGGTTTTCAAGACCGGTGCCTTCAACCGCTCGGCCACACTTCCGGAATGACGCGCACTATAAACATCCCGATGCGGCGTGTAAACCCCTAATTTGTTTGTTTGCCTGAAAAACAGCCAAAAGTGCATTGATAGCGTGAAATAACAGCAGATTGATCATTTCATCACCATGAATTCCTTCTCTTTTACT  >  NC_000913/1031667‑1031857

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑