Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,080,963	A→T	10.2%	intergenic (‑143/+20)	amaC ← / ← dpkA	D‑lysine aminotransferase/delta 1‑piperideine‑2‑carboxylate reductase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,080,963	0	A	T	10.2%	163.5 / 10.5	59	intergenic (‑143/+20)	amaC/dpkA	D‑lysine aminotransferase/delta 1‑piperideine‑2‑carboxylate reductase
Reads supporting (aligned to +/- strand):  ref base A (28/25);  new base T (4/2);  total (32/27)
Fisher's exact test for biased strand distribution p-value = 6.78e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.09e-02

CAGCGTGCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCATGT  >  NC_002947/4080820‑4081110                                                                                                                                                 |                                                                                                                                                    caGCGTGCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCcg                                                                                                                                               <  1:907553/150‑1 (MQ=255)          gCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGc                                                                                                                                      >  2:1088609/1‑150 (MQ=255)            tCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCCCCTTCGCGGGTTTACCCGCGaaaaagcca                                                                                                                                    <  1:1268872/150‑8 (MQ=255)              cTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCaaa                                                                                                                                  >  1:998702/1‑150 (MQ=255)                  gATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAg                                                                                                                              >  2:914127/1‑150 (MQ=255)                   aTCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGc                                                                                                                             <  1:1088609/150‑1 (MQ=255)                   aTCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGc                                                                                                                             >  2:1036198/1‑150 (MQ=255)                    tCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCACAACGGGGCGGAATCAGcc                                                                                                                            >  2:790571/1‑150 (MQ=255)                       ggACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAag                                                                                                                         <  1:1158619/150‑1 (MQ=255)                             tACGGAAAGTCAGTGTTGAGCATACCCGGAGGGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAagcagcgt                                                                                                                   >  2:354369/1‑148 (MQ=255)                                ggAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCttt                                                                                                                >  1:835451/1‑150 (MQ=255)                                     gatcttgtTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGc                                                                                                           <  2:1096867/145‑1 (MQ=255)                                          tgtTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTc                                                                                                      <  1:914127/150‑1 (MQ=255)                                          tgtTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTc                                                                                                      <  2:998702/150‑1 (MQ=255)                                           gtTGAGCATACCCGGAGTGCGGGTTCAGGAACATGAAATAACCTGACAGCTGGTCGATCGCAA‑TGGGCGTGATCTTGATGAGGGATGGATTTTTATCCGGTAAACCCGCTAAGGGGCCAAATCAGCCAAGGAGCTCTTTCAGGccagatc                                                                                                     >  1:1096867/1‑145 (MQ=255)                                            ttGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCcgc                                                                                                                                              <  1:389920/108‑1 (MQ=255)                                            ttGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCcgc                                                                                                                                              >  2:389920/1‑108 (MQ=255)                                            ttGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCa                                                                                                                               >  2:823170/1‑123 (MQ=255)                                            ttGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCa                                                                                                                               <  1:823170/123‑1 (MQ=255)                                                           gTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGctct                                                                                                                  <  2:86077/121‑1 (MQ=255)                                                           gTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGctct                                                                                                                  >  1:86077/1‑121 (MQ=255)                                                               gggTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTc                                                                                                 <  1:503957/134‑1 (MQ=255)                                                               gggTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTc                                                                                                 >  2:503957/1‑134 (MQ=255)                                                                       gAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCttt                                                                                                                >  2:1095136/1‑111 (MQ=255)                                                                       gAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCttt                                                                                                                <  1:1095136/111‑1 (MQ=255)                                                                       gAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAg                                                                                                             >  2:869358/1‑114 (MQ=255)                                                                       gAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAg                                                                                                             <  1:869358/114‑1 (MQ=255)                                                                       gAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCAccccccc                                                                         <  2:835451/150‑3 (MQ=255)                                                                              cACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCg                                                                  >  2:189950/1‑150 (MQ=255)                                                                                      tgCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAAc                                                                                                                                                  <  1:1002460/62‑1 (MQ=255)                                                                                      tgCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAAc                                                                                                                                                  >  2:1002460/1‑62 (MQ=255)                                                                                      tgCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTc                                                          <  1:189950/150‑1 (MQ=255)                                                                                         aaGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAggg                                                                                                                                        >  1:1114212/1‑69 (MQ=255)                                                                                         aaGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAggg                                                                                                                                        <  2:1114212/69‑1 (MQ=255)                                                                                         aaGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCttt                                                                                                       <  2:666233/102‑1 (MQ=255)                                                                                         aaGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCttt                                                                                                       >  1:666233/1‑102 (MQ=255)                                                                                          aGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACGCGCGAAGGGGCCAAATCAGCCAGCCAGCTTCTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCgcgc                                                      >  1:811688/1‑150 (MQ=255)                                                                                           ggTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCg                                                                                   <  2:780272/120‑1 (MQ=255)                                                                                           ggTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCg                                                                                   >  1:780272/1‑120 (MQ=255)                                                                                                   aT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAg                                             <  1:848565/150‑1 (MQ=255)                                                                                                        aaCATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCaa                                                                                                                          <  1:1353914/69‑1 (MQ=255)                                                                                                        aaCATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCaa                                                                                                                          >  2:1353914/1‑69 (MQ=255)                                                                                                                   aCCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGcc                                                               <  1:395266/117‑1 (MQ=255)                                                                                                                   aCCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGcc                                                               >  2:395266/1‑117 (MQ=255)                                                                                                                               gctggctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGCCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGc                  <  1:1036198/150‑1 (MQ=255)                                                                                                                                ctggctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGcc                 >  1:336116/1‑150 (MQ=255)                                                                                                                                 tggctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATGAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGccc                >  1:113346/1‑150 (MQ=255)                                                                                                                                 tggctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTAAACTCCTCCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTAACGGGAGCGCCGCTCGCGCGGCATGCGCGCCAGccc                >  1:583288/1‑150 (MQ=255)                                                                                                                                  ggctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGcccc               >  1:1055464/1‑150 (MQ=255)                                                                                                                                    ctTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCAc             <  2:336116/150‑1 (MQ=255)                                                                                                                                     cccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGcgcc                                         >  1:1190391/4‑121 (MQ=255)                                                                                                                                     cccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGcgcc                                         <  2:1190391/118‑1 (MQ=255)                                                                                                                                     cccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCAcc            >  1:1056747/4‑150 (MQ=255)                                                                                                                                     cccttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCAcc            >  2:1025505/4‑150 (MQ=255)                                                                                                                                       tttCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGc          <  2:1055464/150‑1 (MQ=255)                                                                                                                                        ttCGCGGGTTTACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGcc         >  2:496588/1‑150 (MQ=255)                                                                                                                                              ggTAAACCCGCGAAGGGGCCAAATCAGCCAAGCCACTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCAtg   <  2:113346/150‑1 (MQ=255)                                                                                                                                              ggTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCAtg   >  2:878902/1‑150 (MQ=255)                                                                                                                                               gTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCAtgt  >  1:580719/1‑150 (MQ=255)                                                                                                                                                 |                                                                                                                                                    CAGCGTGCAGCTCCTTGGATCAGGACGGTACGGAAAGTCAGTGTTGAGCATACCCGGAGTGCGGGTTCAGGAACATCCACTATTGTGCAAGGTTGTCTAT‑GCAACATTGCATGACCGGGATGAGGGCTGGCTTTTTCGCGGGTAAACCCGCGAAGGGGCCAAATCAGCCAAGCAGCTCTTTCAGGCCTTTCAACTCCTGCTCGGTCACCGCCACCCCCTCCTCCTCGGCCACCTCGCGCTCACGGTAGCGCCGCTCGCCCGGCATGCGCGTCAGCCCCACCGCCTGCATGT  >  NC_002947/4080820‑4081110

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑