Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	2,163,478	T→A	11.4%	I99N (ATT→AAT)	PP_5482 →	hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	2,163,478	0	T	A	11.4%	92.9 / 5.2	35	I99N (ATT→AAT)	PP_5482	hypothetical protein
Reads supporting (aligned to +/- strand):  ref base T (16/15);  new base A (2/2);  total (18/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.10e-01

CTGGTGCCTGCACTCGAATGCTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGTTTCAACGCTTACACCAGTAAATTTTGG  >  NC_002947/2163345‑2163623                                                                                                                                      |                                                                                                                                                  cTGGTGCCTGCACTCGAATGCTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCta                                                                                                                                   >  1:79380/1‑150 (MQ=255)   ggTGCCTGCACTCGAATGCTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCtata                                                                                                                                 <  2:79380/150‑1 (MQ=255)            aCTCGAATGCTTTAACACGGTAGTCAGTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAAGCATCATTGCTGACTTTCAGCTATATGTGGACCa                                                                                                                        >  2:561951/1‑150 (MQ=255)            aCTCGAATGCTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGc                                                                                                                                             >  1:108628/1‑129 (MQ=255)            aCTCGAATGCTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGc                                                                                                                                             <  2:108628/129‑1 (MQ=255)            aCTCGAATGCTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCa                                                                                                                        >  1:310248/1‑150 (MQ=255)                     cTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCCTTGAAAAGATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTc                                                                                                               <  1:561951/150‑1 (MQ=255)                      tttAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCg                                                                                                              >  2:3344/1‑150 (MQ=255)                         aaaaCGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCAt                                                                                                           <  1:230473/150‑1 (MQ=255)                                  gTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCAATGATGCCt                                                                                                                                           >  2:704055/1‑109 (MQ=255)                                  gTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCAATGATGCCt                                                                                                                                           <  1:704055/109‑1 (MQ=255)                                     aTTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGAt                                                                                               <  1:3344/150‑1 (MQ=255)                                                tAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGtt                                                                                    <  2:279332/150‑1 (MQ=255)                                                  aCGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATCCCAGGTCGTtgt                                                                                  <  2:1035228/150‑1 (MQ=255)                                                     aTGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCa                                                                               <  2:424403/150‑1 (MQ=255)                                                                 tCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGAAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTCTATGTTGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCAc                                                                   >  1:426852/1‑150 (MQ=255)                                                                            aaaaTTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGACGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTAGTGCACCGCAGCCGCACCTAAATTCGCa                                                        <  2:582762/150‑1 (MQ=255)                                                                                ttATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATg                                                                                                                      >  1:336084/1‑84 (MQ=255)                                                                                ttATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATg                                                                                                                      <  2:336084/84‑1 (MQ=255)                                                                                  aTGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCa                                                  <  1:585734/150‑1 (MQ=255)                                                                                    gCTGGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCAtt                                                <  2:811780/150‑1 (MQ=255)                                                                                              gCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACg                                      >  1:32603/1‑150 (MQ=255)                                                                                                tCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGt                                    >  1:32963/1‑150 (MQ=255)                                                                                                      gCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAg                                                       <  1:380839/125‑1 (MQ=255)                                                                                                      gCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAg                                                       >  2:380839/1‑125 (MQ=255)                                                                                                      gCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAGACTACGGTTGAAAg                              >  1:100999/1‑150 (MQ=255)                                                                                                        aGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGtt                            >  1:1027040/1‑150 (MQ=255)                                                                                                            aCTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGTTTCaa                        <  2:1027040/150‑1 (MQ=255)                                                                                                             cTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAGACTACGGTTGAAAGTTTCAAc                       <  2:100999/150‑1 (MQ=255)                                                                                                              tCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGTTTCAACg                      >  2:1063554/1‑150 (MQ=255)                                                                                                                gAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGTTTCAACGCt                    >  1:62987/1‑150 (MQ=255)                                                                                                                   ttCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGTTTCAACGCTTac                 >  2:285080/1‑150 (MQ=255)                                                                                                                          tgaaaGGCATCAATGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAATGTTTCAACGCTTa                  <  2:318520/139‑1 (MQ=255)                                                                                                                          tgaaaGGCATCAATGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAATGTTTCAACGCTTa                  >  1:318520/4‑142 (MQ=255)                                                                                                                             aaGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCACTTGAAACTACGGTTGAAAGTTTCAACGCTTACACCAGTAAAt       >  2:376770/1‑150 (MQ=255)                                                                                                                                  atcatTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGTTTCAACGCTTACACCAGTAAATTTTgg  >  2:1084017/1‑150 (MQ=255)                                                                                                                                      |                                                                                                                                                  CTGGTGCCTGCACTCGAATGCTTTAAAACGGTAGTCATTGAGCGAAATAACGATGAGCGTGTTATCGCAGCCATCAAAATTATGCTTGACGAGGCTCGTAGGCAGGAACTCGAATTCGAGTATGAAGGCATCATTGATGCCTTTCAGCTATATGTGGACCATGGCGACTCGCATTCGTTGCTGGATACCAGGTCGTTGTGCACCGCAGCCGCACCTAAATTCGCAGCGGCATTTGAAACTACGGTTGAAAGTTTCAACGCTTACACCAGTAAATTTTGG  >  NC_002947/2163345‑2163623

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑