Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	1,212,521	C→T	100%	intergenic (‑55/+133)	PP_1060 ← / ← PP_1061	glutamate synthase large subunit/ATP‑dependent DNA helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	1,212,521	0	C	T	100.0%	177.0 / ‑6.8	54	intergenic (‑55/+133)	PP_1060/PP_1061	glutamate synthase large subunit/ATP‑dependent DNA helicase
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (24/29);  minor base A (1/0);  total (25/29)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CATTCGTGGTGGCTGAAGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACCATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCCGCCGCTACCGTATTC  >  NC_002947/1212378‑1212664                                                                                                                                                |                                                                                                                                                cATTCGTGGTGGCTGAAGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGc                                                                                                                                            <  4:47132/149‑1 (MQ=255)  aTTCGTGGTGGCTGAAGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGc                                                                                                                                            >  7:260701/1‑148 (MQ=255)            gCTGAAGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCgg                                                                                                                                 <  2:189384/149‑1 (MQ=255)              tGAAGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACtata                                                                                                                                              <  1:174145/134‑1 (MQ=255)              tGAAGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACtata                                                                                                                                              >  2:174145/1‑134 (MQ=255)                aaGGGGAGGCTCGCCAGGGTGAACAGCACACATGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGGCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCa                                                                                                                              <  5:291895/148‑1 (MQ=255)                aaGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCAc                                                                                                                             >  3:371875/1‑149 (MQ=255)                     gAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCaa                                                                                                                                         >  7:329825/1‑132 (MQ=255)                     gAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCaa                                                                                                                                         <  8:329825/132‑1 (MQ=255)                        gCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCaaaa                                                                                                                      >  5:148885/1‑148 (MQ=255)                            gCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCaaaataaaa                                                                                                                 <  7:26141/149‑1 (MQ=255)                                 ggTGAACAGCACACAGGCGGCGAAGAAGGCATAACGTCTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCggg                                                                                                            <  4:271227/149‑1 (MQ=255)                                 ggTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCggg                                                                                                            <  4:324747/149‑1 (MQ=255)                                 ggTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCggg                                                                                                            <  2:223070/149‑1 (MQ=255)                                           accaaGGCGGCGAAGAAGGCATAACGACTGATAAGTGACAGGCTCATACAGGCTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGaaaa                                                                                                  <  6:26290/145‑1 (MQ=255)                                           acacaGGCCGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAACCCCCGACAATAGCCAAGTCGCCGGGCACGGCAAAAAAAAATCGGCGTACCGaaa                                                                                                   >  8:67970/1‑148 (MQ=255)                                             acaGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAAt                                                                                                 >  1:189769/1‑148 (MQ=255)                                              caGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATTGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGCTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCa                                                                                               <  5:98893/149‑1 (MQ=255)                                                   ggcgAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATtctc                                                                                          >  7:147929/1‑149 (MQ=255)                                                     cgAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGa                                                                                        <  8:260701/149‑1 (MQ=255)                                                      gaagaaGGTATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATtc                                                                                            >  7:339305/1‑144 (MQ=255)                                                      gaagaaGGTATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATtc                                                                                            <  8:339305/144‑1 (MQ=255)                                                         gaagGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCg                                                                                     >  2:7329/1‑148 (MQ=255)                                                               aTAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGc                                                                              >  5:155483/1‑149 (MQ=255)                                                                  aCGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCGAAGTTGCCGGGCACTGCAAAATAAAATGGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCgg                                                                            <  4:146343/148‑1 (MQ=255)                                                                  aCGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCgg                                                                            <  1:105924/148‑1 (MQ=255)                                                                       tGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCAc                                                                      >  8:219910/1‑149 (MQ=255)                                                                         agaAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCAccc                                                                    >  1:208832/1‑149 (MQ=255)                                                                         agaAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCAccc                                                                    <  8:147929/149‑1 (MQ=255)                                                                           aaGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCcgc                                                                  <  2:208832/149‑1 (MQ=255)                                                                                 cAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAgg                                                            <  4:371875/149‑1 (MQ=255)                                                                                      tCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAgggccgg                                                       >  8:252668/1‑149 (MQ=255)                                                                                            aGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCctg                                                  >  6:2470/1‑148 (MQ=255)                                                                                            aGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCctg                                                  <  5:2470/148‑1 (MQ=255)                                                                                             gggTCCTTGCGATGGCGGGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTCGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCctgct                                                <  7:67970/149‑1 (MQ=255)                                                                                              ggTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAg                                                                                  <  3:275027/114‑1 (MQ=255)                                                                                              ggTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAg                                                                                  >  4:275027/1‑114 (MQ=255)                                                                                               gTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTTTAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTgg                                              >  4:35429/1‑149 (MQ=255)                                                                                                 ccTTGCCATGGCGCGGTCAGGCTCAGCGCCTGGGGGCAAACCCCGACTATAGACAAGTTGCCGGGCACTGCAAAATAAAATCGGGCTACCGAAAATCATTCTCGAGCGTAGGAGCGCGTTCACCCGCGAAAGGGCCGGGCCTGCTGGc                                             >  8:61985/1‑148 (MQ=38)                                                                                                            cgcgGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCAccc                                 >  8:70698/1‑149 (MQ=255)                                                                                                                   aGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAATTCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCAGCAGGcccggc                                        >  4:156737/1‑131 (MQ=39)                                                                                                                   aGGCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAATTCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCAGCAGGcccggc                                        <  3:156737/135‑5 (MQ=39)                                                                                                                     gCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCggg                                                                                                            <  6:361678/65‑1 (MQ=255)                                                                                                                     gCTCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCggg                                                                                                            >  5:361678/1‑65 (MQ=255)                                                                                                                       tCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGaaa                                                              >  8:58229/1‑109 (MQ=255)                                                                                                                       tCAGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGaaa                                                              <  7:58229/109‑1 (MQ=255)                                                                                                                         aGGGCCTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGtt                    >  1:284356/1‑149 (MQ=255)                                                                                                                              cTGGGGGCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTgccgc               <  2:284356/149‑1 (MQ=255)                                                                                                                                 ggggCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCcgccgc            <  6:148885/149‑1 (MQ=255)                                                                                                                                 ggggCAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCcgccgc            <  1:7329/149‑1 (MQ=255)                                                                                                                                     cAAACCCCGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCCGCCGCTAcc        <  7:252668/149‑1 (MQ=255)                                                                                                                                          cccGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCCGCCGCTACCGTAtt   >  6:50458/1‑149 (MQ=255)                                                                                                                                           ccGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGccgccg             <  4:269048/138‑1 (MQ=255)                                                                                                                                           ccGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGccgccg             >  3:269048/1‑138 (MQ=255)                                                                                                                                           ccGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCCGCCGCTACCGTATTc  <  6:157479/149‑1 (MQ=255)                                                                                                                                            cGACTATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCCGCCGCTACCgcct    >  8:186949/1‑143 (MQ=255)                                                                                                                                                |                                                                                                                                                CATTCGTGGTGGCTGAAGGGGAGGCTCGCCAGGGTGAACAGCACACAGGCGGCGAAGAAGGCATAACGACTGAGAAGTGACAGGCTCATACAGGGTCCTTGCGATGGCGCGGTCAGGCTCAGGGCCTGGGGGCAAACCCCGACCATAGCCAAGTTGCCGGGCACTGCAAAATAAAATCGGGGTAGCGAAAATCATTCTCGAGCGTAGGAGCGGGTTCACCCGCGAAAGGGCCGGGCCTGCTGGCCAATCTCCACCCGCCGTGCACCGTTGCCGCCGCTACCGTATTC  >  NC_002947/1212378‑1212664

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑