Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_014034	2,995,614	+C	10.0%	intergenic (+154/+66)	RCAP_rcc02802 → / ← RCAP_rcc02803	membrane dipeptidase/hypothetical protein

Read alignment evidence...
	seq id	position		change	freq	score	reads	annotation	genes	product
*	NC_014034	2,995,614	1	.→C	10.0%	4.4 ‑2.4 ‑1.3	30	intergenic (+154/+66)	RCAP_rcc02802/RCAP_rcc02803	membrane dipeptidase/hypothetical protein
Reads supporting (aligned to +/- strand):  new base (3/0):  ref base (11/16):  total (14/16)
Fisher's exact test strand distribution p-value = 8.97e-02
Kolmogorov-Smirnov test that lower quality scores support polymorphism than reference p-value = 5.17e-02

CCGGACCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCT  >  NC_014034/2995514‑2995702                                                                                                      |                                                                                            ccGGACCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACg                                                                                              <  2:299489/101‑1 (MQ=255)  cGGACCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.c                                                                                            <  1:4200245/101‑1 (MQ=255)  cGGACCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.c                                                                                            <  1:4195580/101‑1 (MQ=255)  cGGACCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.c                                                                                            <  1:4084807/101‑1 (MQ=255)   cgACCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.cc                                                                                           <  2:615335/100‑1 (MQ=255)     aCCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCgg                                                                                         <  1:664571/101‑1 (MQ=255)        cccAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCggggg                                                                                      <  2:1881066/101‑1 (MQ=255)        cccAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCggggg                                                                                      <  2:2970744/101‑1 (MQ=255)         ccAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCgggggg                                                                                     <  2:2664956/101‑1 (MQ=255)           aaGGGGCGTATTTTGCCAAGAAACCCCCCTTCGGTTGCCGCCCCCCACCCCGTCGGCGGCCCAGCGCCCTTCTTTTCCTGGGCAAAATACG.CCGGGGGGTg                                                                                   <  2:136916/101‑1 (MQ=37)           aaGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTg                                                                                   <  1:2101022/101‑1 (MQ=255)           aaGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTg                                                                                   <  2:2098652/101‑1 (MQ=255)                 cGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCggggg                                                                             <  2:3452114/101‑1 (MQ=255)                   tATTTTGCCAAGGAAACCCCCTTCGGTTGCCGCCCCGCAACCCTTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGc                                                                           <  2:3093288/101‑1 (MQ=255)                    tttttGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCg                                                                          <  2:3465056/100‑1 (MQ=255)                      tttGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGa                                                                        <  2:2827920/101‑1 (MQ=255)                      tttGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGa                                                                        <  2:1780930/101‑1 (MQ=255)                       ttGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAg                                                                       >  1:889266/1‑101 (MQ=255)                          ccAAGGAAACCCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGccc                                                                    <  2:1882955/101‑1 (MQ=255)                          ccAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCggttccc                                                                    <  2:137755/101‑6 (MQ=255)                          ccAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGccc                                                                    <  2:2332391/101‑1 (MQ=255)                            aaGGAAACCCCCTTCGTTTGCCGCCCCGCACCCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGAAAAATACG.CCGGGGGGTGCGGGGGGCGGAGccccc                                                                  <  2:1510146/101‑1 (MQ=25)                                   aCCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.Cgggc                                                          >  1:2832347/1‑100 (MQ=255)                                       cTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGcc                                                      >  1:2252209/1‑101 (MQ=255)                                        ttgggTTGCCGCCCCGCACCCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CGGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGccc                                                     <  2:586805/98‑1 (MQ=255)                                                       gCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCCGGGCg                                    >  1:94853/1‑101 (MQ=255)                                                        cAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCggggggg                                   >  1:4006701/1‑98 (MQ=255)                                                         aaCCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGaa                                  >  1:3498010/1‑101 (MQ=255)                                                              gTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATccc                             >  1:3112198/1‑101 (MQ=255)                                                                cggcggCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGGAATccccc                           >  2:1978130/1‑101 (MQ=255)                                                                          gcgcCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTccc                 >  2:432538/1‑101 (MQ=255)                                                                               ttgtttttCCTTGGAAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAGCccttc               >  2:1285997/5‑98 (MQ=0)                                                                                   ttttCCTTGGAAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAGCccttcatct           >  2:4195359/1‑94 (MQ=2)                                                                                     ttCCTTGGAAAAATACGCCCGGGGGGTGCGGGGGGCGGAGCCCCCCGCCGGGTCGCCTCGGCGTCAGCCGAGGCGAAATACCCC.CTCAGCccttcatcttg         >  1:3319971/1‑92 (MQ=0)                                                                                      tCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGa     >  1:1538854/1‑101 (MQ=255)                                                                                         ttGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCt  >  1:3327980/1‑101 (MQ=255)                                                                                                      |                                                                                            CCGGACCCCCAAGAGGCGTATTTTGCCAAGGAAAACCCCTTCGGTTGCCGCCCCGCAACCCGTCGGCGGCCCAGCGCCCTGCTTTTCCTTGGCAAAATACG.CCGGGGGGTGCGGGGGGCGGAGCCCCCCG.CGGGTCGCCCCGGCTT..GCCGGGGCGAAATCCCCCGCTCAGTCCCAGAGACTTTCGACCT  >  NC_014034/2995514‑2995702 Base quality scores:  ATCG  < 3 ≤  ATCG  < 15 ≤  ATCG  < 25 ≤  ATCG  < 33 ≤  ATCG  < 40 ≤  ATCG