Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	974,303	+G	84.2%	intergenic (+183/+76)	RCAP_rcc00884 → / ← RCAP_rcc00885	hypothetical protein/hypothetical protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	974,303	1	.→G	84.2%	3.8 ‑0.7 ‑1.0	19	intergenic (+183/+76)	RCAP_rcc00884/RCAP_rcc00885	hypothetical protein/hypothetical protein
Reads supporting (aligned to +/- strand):  new base (6/10):  ref base (0/3):  total (6/13)
Fisher's exact test strand distribution p-value = 5.17e-01
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 1.06e-01

CCCCGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CG.TGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.GGGG...T...GTGCG.....GAAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCCGCCGCAACGGCCGGTTCTCAG  >  NC_014034/974204‑974382                                                                                                        |                                                                                           ccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCCCCTTGCGGCAAATATcc.c                                                                                             >  1:6850228/1‑101 (MQ=39) ccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc.c                                                                                             >  1:1392318/1‑101 (MQ=255) ccccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc.c                                                                                             >  1:4568230/1‑101 (MQ=255)  cccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.g                                                                                           >  1:8296522/1‑101 (MQ=255)   ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTACCTTGCGACACATATcc.ccg                                                                                           >  2:6157328/1‑99 (MQ=38)   ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTACCTTGCGACAAATATcc.ccg                                                                                           >  1:5115438/1‑99 (MQ=255)   ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATcc.ccg                                                                                           >  1:3592506/1‑99 (MQ=255)   ccGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCCTGTCGCAAATATtc.ccg                                                                                           >  2:3204601/1‑99 (MQ=37)    cGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggg                                                                                         >  2:9160570/1‑101 (MQ=255)    cGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAAAATCC.C.ggg                                                                                         >  1:4896942/1‑101 (MQ=255)     ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTCCCTTGCGAACAATATCC.C.gggg                                                                                        >  2:2677963/1‑101 (MQ=38)     ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCCCCCTTCGACAAATATAC.C.cggg                                                                                        >  1:1077670/1‑101 (MQ=37)     ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATTC.C.gggg                                                                                        >  2:6143285/1‑101 (MQ=255)     ggACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggg                                                                                        >  2:1447569/1‑101 (MQ=255)      gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  1:4545441/1‑100 (MQ=255)      gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  2:6884226/1‑100 (MQ=255)      gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  1:7113758/1‑100 (MQ=255)      gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       <  1:6958062/101‑2 (MQ=255)      gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  2:7845050/1‑100 (MQ=255)      gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggg                                                                                       >  1:4832796/1‑100 (MQ=255)      gACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cgggg                                                                                       >  1:715269/1‑100 (MQ=255)       gccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggt                                                                                      <  2:8972899/100‑3 (MQ=255)       aCCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cggggt                                                                                      >  2:1725297/1‑99 (MQ=255)        ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtc                                                                                     <  2:4873486/101‑4 (MQ=255)        ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtc                                                                                     <  1:2358036/101‑4 (MQ=255)        ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtc                                                                                     <  1:4571081/101‑4 (MQ=255)        ccccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cggggtc                                                                                     >  1:2323734/1‑98 (MQ=38)         cccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtcc                                                                                    <  1:6143522/101‑5 (MQ=255)         cccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtcc                                                                                    <  1:1725350/101‑5 (MQ=255)          ccccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccg                                                                                   <  1:6841177/101‑6 (MQ=255)           cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgg                                                                                  <  2:3485095/101‑7 (MQ=39)           cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgg                                                                                  <  2:4896782/101‑7 (MQ=39)           cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgg                                                                                  <  2:7756647/101‑7 (MQ=39)           cccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.cggggtccgg                                                                                  >  1:1339272/1‑95 (MQ=38)            ccAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTTACCTTGCGACAAATATCC.C.ggggggccggg                                                                                 >  1:86867/1‑94 (MQ=38)             cAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgggg                                                                                <  2:313528/101‑9 (MQ=38)               gCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgggggc                                                                              <  2:2323667/101‑11 (MQ=38)               gCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.gggggtccgggggc                                                                              <  1:727450/101‑11 (MQ=38)               gCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.ggggggccgggggc                                                                              >  1:2085746/1‑91 (MQ=38)                                    gCAGCCGGGCGGGATGCGCAATGCC.CGCTGCGCAGCGGCTTGTTTACACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCt                                                  <  2:9111592/101‑1 (MQ=0)                                      agccgggcgggATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATA.CC.C.GGGG...G...GTCCGGGGGCGGAGCCCCCGGCGGGTCGCCTCg                                                <  2:6849956/98‑1 (MQ=9)                                             cgggACCCGGCATGGCGTC.TGGGCGGCGGCTTTTTTTCTCCTTGCGACAAATACCC.CGGGGG...TCC.GGGGGC....GGACCCCCCGGCGGGTCGCCTCGGCGACAg                                         <  1:8484935/101‑1 (MQ=2)                                                gATCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCCCCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCg                                      <  1:2806748/101‑1 (MQ=9)                                                  tCCGTCATGGC.CGCTGCACAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAg                                    <  2:1611338/101‑1 (MQ=2)                                                  tCCGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAg                                    <  2:2486427/101‑1 (MQ=11)                                                    cGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCCGG.GGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGc                                  <  2:3760642/101‑1 (MQ=2)                                                    cGGCATGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGc                                  <  1:1641537/101‑1 (MQ=11)                                                        aTGGC.CGCTGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGaaa                              <  2:3424245/101‑1 (MQ=11)                                                            gccgctGCGCAGCGGCTTGTATTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACTGCCGAGGCGCACTAc                           <  1:8834430/96‑1 (MQ=2)                                                               gctGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATAcccc                        <  2:4958861/99‑1 (MQ=11)                                                                   cgcACCGGCTTGTTTCCCCCTGGCGACAAATATCCGG.GGGG...TCG.GGGGGC....GGACCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCcggcc                    <  2:5815710/101‑1 (MQ=2)                                                                         ggCTTGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACg              <  2:7252201/101‑1 (MQ=11)                                                                           tttGTTTCCGCCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACGGc            <  1:6945617/100‑1 (MQ=2)                                                                            ttGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGCGCCGCCGCGGCCGCCGCGGGGGAAAACACCCGCCCCCACCGcc           >  2:6319615/1‑101 (MQ=0)                                                                             tGTTTTCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGGGGCGCGGCGGCAGCCGCGGGGGAATAACCCCCCCCCACCGGCCg          >  2:6888089/1‑101 (MQ=0)                                                                                 ttCACCTTGCGACAAATATCC.CGGGGG...TCCGGTGGC.....GGAGCCCCCGGCGGGGGGCGCCGGCGCCAGACGGGGCGGAAGAAACCGGCCGCAACGGCCggggg      >  1:1533918/1‑98 (MQ=0)                                                                                  tCACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGGGCCTCGGCGGCCGCCGCGGGGGAAGAACCCCGCCGCCACCGCCGGGtct     >  1:1807081/1‑101 (MQ=2)                                                                                  tCACCTTGCGACAAATAGCC.C.GGGGGGCC...GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACGGCCGGTtct     <  1:5294916/101‑1 (MQ=2)                                                                                   cACCTTGCGACAAATATCC.G.GGGGGCCC...GGGGGC....GGAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCGGCCGCAACGGCCGGTtctc    <  2:1469899/101‑1 (MQ=2)                                                                                   cACCTTGCGACAAATATCC.CGGGGG...TCC.GGGGGC....GGAGCCCCCGGCGGGGCGGCCCGGCGACCGCCGCGGCGGAAAACCCCGGCCGCCCCGGcacggtcgc    >  2:8178717/1‑93 (MQ=2)                                                                                     ccTTGCGACAAATATCC.CGGGGG...TCCGGGGGC.....GGAGCCCCCGGCGGGGGGCCTCGGGGGCAGCCGCGGCGGAAAAACACCGCCGCCCCAGCCgggcccccc  >  2:3614922/1‑94 (MQ=2)                                                                                                        |                                                                                           CCCCGGACCCCCCAGCGTATTTGCACCAAGAAAAAGCAGACGGGCGGGATCCGGCATGGC.CG.TGCGCAGCGGCTTGTTTTCACCTTGCGACAAATATCC.C.GGGG...T...GTGCG.....GAAGCCCCCGGCGGGTCGCCTCGGCGACAGCCGAGGCGAAATACCCCCGCCGCAACGGCCGGTTCTCAG  >  NC_014034/974204‑974382 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 24 ≤  ATCG  < 33 ≤  ATCG  < 41 ≤  ATCG