Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	4,184,912	A→T	10.5%	R230S (AGA→AGT)	PP_3681 →	putative Helicase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	4,184,912	0	A	T	10.5%	96.2 / 3.9	38	R230S (AGA→AGT)	PP_3681	putative Helicase
Reads supporting (aligned to +/- strand):  ref base A (20/14);  new base T (2/2);  total (22/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.38e-01

ATCCACCTCACCGCGGTCGGAGATCGCAAGCAAATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTCCAGCACTCTTCACAAGAAGCGACCGTGCTT  >  NC_002947/4184784‑4185059                                                                                                                                 |                                                                                                                                                    aTCCACCTCACCGCGGTCGGAGATCGCAAGCAAATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACg                                                                                                                                 >  5:226874/1‑149 (MQ=255)       cTCACCGCGGTCGGAGATCGCAAGCAAATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCa                                                                                                                           <  1:289172/149‑1 (MQ=255)          aCCGCGGTCGGAGATCGCAAGCAAATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGCACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGaa                                                                                                                        <  4:128337/149‑1 (MQ=255)                gTCGGAGATCGCAAGCAAATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCCCCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAat                                                                                                                  >  2:300070/1‑149 (MQ=255)                  cGGAGATCGCAAGCAAATGATCATGGGGTCGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAatca                                                                                                                >  7:157968/1‑149 (MQ=255)                   ggAGATCGCAAGCAAATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCGCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAatcat                                                                                                               >  8:12115/1‑149 (MQ=255)                            aagcaaATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAAt                                                                                                      >  8:111/1‑149 (MQ=255)                                aaaTGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGAc                                                                                                  <  3:1348/149‑1 (MQ=255)                                  aTGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGAGACTGACTTCGATGCCCTACCACTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGAccc                                                                                                >  5:40920/1‑149 (MQ=255)                                           gggTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTcagcag                                                                                        <  8:95569/148‑1 (MQ=255)                                                     gAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGa                                                                                     <  6:308375/141‑1 (MQ=255)                                                     gAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGa                                                                                     >  5:308375/1‑141 (MQ=255)                                                        cgcTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGaa                                                                          <  8:157968/149‑1 (MQ=255)                                                           tGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGTTCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGc                                                                                  >  5:201602/1‑138 (MQ=255)                                                           tGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGTTCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGc                                                                                  >  5:206065/1‑138 (MQ=255)                                                           tGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGTTCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGc                                                                                  <  6:206065/138‑1 (MQ=255)                                                           tGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGTTCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGc                                                                                  <  6:201602/138‑1 (MQ=255)                                                             gAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTg                                                                       <  6:226874/147‑1 (MQ=255)                                                                        cAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGtga                                                            <  4:138728/147‑1 (MQ=255)                                                                                     actgactTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGaa                                                                          >  8:232950/1‑120 (MQ=255)                                                                                           ttCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGt                                       >  6:128462/1‑149 (MQ=255)                                                                                           ttCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGt                                       >  6:10332/1‑149 (MQ=255)                                                                                           ttCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGt                                       >  3:155314/1‑149 (MQ=255)                                                                                           ttCGATGCCCTACCCCGCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGt                                       <  7:12115/149‑1 (MQ=255)                                                                                                 gCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCAttt                                 >  1:116838/1‑149 (MQ=255)                                                                                                   ccTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTc                                >  8:54328/1‑148 (MQ=255)                                                                                                   ccTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTc                                >  8:273005/1‑148 (MQ=255)                                                                                                    cTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTCCa                              <  6:40920/149‑1 (MQ=255)                                                                                                     tACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTCCAg                             <  2:116838/149‑1 (MQ=255)                                                                                                                 tGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCgg                                                                >  7:1841/1‑102 (MQ=255)                                                                                                                 tGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCgg                                                                <  8:1841/102‑1 (MQ=255)                                                                                                                     cGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGga                                                     <  1:166275/109‑1 (MQ=255)                                                                                                                     cGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGga                                                     >  2:166275/1‑109 (MQ=255)                                                                                                                        aaaTTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGAAGTTCATTTCCAGCACTCTTCACAAGAAGCGa          >  3:99350/1‑149 (MQ=255)                                                                                                                           tttCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAATTTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCggg                                                               >  7:274757/1‑93 (MQ=255)                                                                                                                           tttCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCggg                                                               <  8:274757/93‑1 (MQ=255)                                                                                                                           tttCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTCCAGCACTCTTCACAAGAAGCGACCg       >  3:169382/1‑149 (MQ=255)                                                                                                                                gATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTCCAGCACTCTTCACAAGAAGCGACCGtgctt  >  5:216415/1‑149 (MQ=255)                                                                                                                                 |                                                                                                                                                    ATCCACCTCACCGCGGTCGGAGATCGCAAGCAAATGATCATGGGGTGGGCGGGAGCGCTGGAGGGCATCTTCAAGACGTATGCGACTGACTTCGATGCCCTACCCCTCCACCTGTACGCAAATTTCAGATCGAAGTCCAATCTGCTACGTGTTCAGAATGAAATCATCCGTGAAATTGACCCCTCAGCAGTGACGCCAGCAGAACTGATCTCGGGTGATGAGGGAGAGGTCTTGGCAGTTCATTTCCAGCACTCTTCACAAGAAGCGACCGTGCTT  >  NC_002947/4184784‑4185059

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑