Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,369,021	A→G	9.7%	N776S (AAT→AGT) ‡	PP_2964 →	transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,369,021	0	A	G	9.7%	109.9 / 2.9	41	N776S (AAT→AGT) ‡	PP_2964	transposase
Reads supporting (aligned to +/- strand):  ref base A (19/18);  new base G (2/2);  total (21/20)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.79e-01

TTCATCCCGCCGGGCATCTGGGAGGCGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTGATGCAGGTCGCA  >  NC_002947/3368876‑3369169                                                                                                                                                  |                                                                                                                                                     ttCATCCCGCCGGGCATCTGGGAGGCGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCt                                                                                                                                                   >  4:222270/1‑149 (MQ=255)    aTCCCGCCGGGCATCTGGGAGGCGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGAt                                                                                                                                                >  2:278702/1‑149 (MQ=255)     tCCCGCCGGGCATCTGGGAGGCGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATg                                                                                                                                               >  5:101129/1‑149 (MQ=255)     tCCCGCCGGGCATCTGGGAGGCGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATg                                                                                                                                               <  4:222017/149‑1 (MQ=255)                aTCTGGGAGGCGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGACACGTATTct                                                                                                                                    >  6:35745/1‑148 (MQ=255)                          cGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGgcgc                                                                                                                          <  4:300125/149‑1 (MQ=255)                                         aGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTgc                                                                                                           >  4:230300/1‑149 (MQ=255)                                           gggCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTgccg                                                                                                         >  6:167951/1‑149 (MQ=255)                                                 ctCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTgccggccg                                                                                                     <  1:278702/147‑1 (MQ=255)                                                   cAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATc                                                                                                 >  6:56358/1‑149 (MQ=255)                                                      ggCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATcgcg                                                                                              <  8:287350/149‑1 (MQ=255)                                                       gCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCgg                                                                                             >  8:150908/1‑149 (MQ=255)                                                       cttGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATcgcg                                                                                              <  5:266076/146‑1 (MQ=255)                                                          gATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATcgcc                                                                                              >  6:266076/1‑144 (MQ=255)                                                           aTCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTg                                                                                           <  8:83903/147‑1 (MQ=255)                                                                accGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCAACGCTGTTTGACTTCACCCATCTGATGGGCATCAATCTGATGCCACGTATTCGAAACTGGCGCGACCTGGTGATTTGCAGGCCGGATCGCCGTTCTTCGTa                                                                                    >  8:66903/3‑149 (MQ=255)                                                                  cGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTAt                                                                                                                                       >  2:102782/1‑96 (MQ=255)                                                                    tCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAg                                                                                <  5:56358/149‑1 (MQ=255)                                                                         gCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCatat                                                                           <  7:150908/149‑1 (MQ=255)                                                                         gCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCata                                                                            <  5:35745/148‑1 (MQ=255)                                                                            gACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGtg                                                                                    >  1:106542/1‑136 (MQ=255)                                                                            gACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTa                                                                                    <  2:106542/137‑1 (MQ=255)                                                                                        tCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCAc                                                            >  3:112762/1‑149 (MQ=255)                                                                                              aCCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGacac                                                      >  6:301790/1‑149 (MQ=255)                                                                                                ccAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACaa                                                                                 <  8:39311/120‑1 (MQ=255)                                                                                                ccAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACaa                                                                                 >  7:39311/1‑120 (MQ=255)                                                                                                ccAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTg                                                    >  2:92168/1‑149 (MQ=255)                                                                                                  aaGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGcc                                                  <  5:301790/149‑1 (MQ=255)                                                                                                            ggCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACt                                        <  5:167951/149‑1 (MQ=255)                                                                                                                 cGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATc                                   <  3:230300/149‑1 (MQ=255)                                                                                                                   gtgtTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCg                                  >  8:230089/1‑148 (MQ=255)                                                                                                                           cTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTGCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACt                         <  4:112762/149‑1 (MQ=255)                                                                                                                              cACCCATCTGTTGTGCATCTATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTg                        <  7:66903/147‑1 (MQ=255)                                                                                                                                 ccATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAg                    >  5:279919/1‑148 (MQ=255)                                                                                                                                        cgtggCATCAGATTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTGAt            <  2:227404/146‑1 (MQ=255)                                                                                                                                         gtggCATCAGATTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGaa                                >  1:301692/3‑128 (MQ=255)                                                                                                                                         gtggCATCAGATTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGaa                                <  2:301692/126‑1 (MQ=255)                                                                                                                                         gtggCATCAGATTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTGATg           >  5:294343/3‑149 (MQ=255)                                                                                                                                            gCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTg              >  2:244713/1‑143 (MQ=255)                                                                                                                                            gCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTg              <  1:244713/143‑1 (MQ=255)                                                                                                                                             cATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTGATGCAgg       <  6:54994/149‑1 (MQ=255)                                                                                                                                                 aaTCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTGATGCAGGTCg    <  6:279919/148‑1 (MQ=255)                                                                                                                                                  aTCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTGATGCAGGTCGCa  >  4:264355/1‑149 (MQ=255)                                                                                                                                                  |                                                                                                                                                     TTCATCCCGCCGGGCATCTGGGAGGCGATCTACGTGATCGAGGGGCTGCTCAAGGCTGATCTCAGCGTCGAGGCTGACACGGTGTACTCCGATACCCAAGGGCAGTCGGCCACGGTGTTTGCCTTCACCCATCTGTTGGGCATCAATCTGATGCCACGTATTCGCAACTGGCGCGACCTGGTGATGTGCCGGCCGGATCGCGGTGCTTCGTACAAGCATATCAACCGCCTGTTCACCGACACTGCCGACTGGAACTTGATCGAAACCCACTGGCAGGATCTGATGCAGGTCGCA  >  NC_002947/3368876‑3369169

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: ‑