Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,968,923	C→T	10.4%	S336F (TCC→TTC)	PP_3498 →	transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,968,923	0	C	T	10.4%	107.6 / 6.1	48	S336F (TCC→TTC)	PP_3498	transposase
Reads supporting (aligned to +/- strand):  ref base C (24/19);  new base T (3/2);  total (27/21)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 6.16e-01

CCGATCAGCACAGCAGCGGAAACAAAATCAGATTGGGCAAGATGAGCAAGCGCGGTGACGGCTACATACGCAGCCTGATGATCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACCGAACGAAAA  >  NC_002947/3968800‑3969070                                                                                                                            |                                                                                                                                                       gcgcctagcgccccggtggcattacccggttggtcagaggctcatagccgcctccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccatataatccgcaGATTCCGATCAGCCAGA‑TGATCGCCGCctct                                                                                                                             <  1:1981719‑M1/31‑1 (MQ=255)                     attacccggttggtcagaggctcatagccgcctccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccatataatccgcaGATTTCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCtt                                                                                                         <  2:1855486‑M1/51‑1 (MQ=255)                                ggtcagaggctcatagccgcctccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccatataatccgcaGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAagga                                                                                              >  2:1981719‑M1/89‑150 (MQ=255)                                    agaggctcatagccgcctccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccatataatccgcaGATTTCGATTAGCCAGCCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAggc                                                                                           >  1:2147869‑M1/85‑150 (MQ=255)                                                ccgcctccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccatacaatccgcaGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAggctg                                                                              >  2:134743‑M1/73‑150 (MQ=255)                                                     tccggtttttcgttcggtttgcgttggtaaacctgatcgctctgtaacagggcccatataatccgcaGATTTCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTaa                                                                         >  1:1855486‑M1/68‑150 (MQ=255)                                                                         gCCTGATGATCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTatat                                                   <  2:1506163/150‑1 (MQ=31)                                                                           gttggtaaacctgatcgctctgtaacagggcccagataatccgcaGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAaggagg                                                                                            <  1:1223781‑M1/64‑1 (MQ=255)                                                                           gttggtaaacctgatcgctctgtaacagggcccagataatccgcaGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAaggagg                                                                                            >  2:1223781‑M1/46‑109 (MQ=255)                                                                           cTGGTGATCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTTTTGCGCTGGCTATCCCGCCTTGGGGGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATgg                                                 <  1:227348/150‑1 (MQ=12)                                                                            tgatgaTCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGCGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATggg                                                >  1:271554/1‑150 (MQ=17)                                                                             gatgatCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGc                                               <  1:1903078/150‑1 (MQ=32)                                                                             gatgatCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGc                                               >  2:136303/1‑150 (MQ=32)                                                                              atgatCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGcc                                              >  2:1020725/1‑150 (MQ=32)                                                                                 atCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTg                                           <  1:132800/150‑1 (MQ=32)                                                                                     aGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGccc                                             >  1:93862/1‑144 (MQ=32)                                                                                     aGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGccc                                             <  2:93862/144‑1 (MQ=32)                                                                                       ggCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACag                                     >  2:1154730/1‑150 (MQ=32)                                                                                          gcgcATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGc                                  <  1:3130/150‑1 (MQ=32)                                                                                            gcATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATg                                                  <  1:126921/132‑1 (MQ=32)                                                                                            gcATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATg                                                  >  2:126921/1‑132 (MQ=32)                                                                                            gcATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGa                                >  1:2137696/1‑150 (MQ=32)                                                                                            gcATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGa                                >  2:1160828/1‑150 (MQ=32)                                                                                            gcATTCCGTCGTTAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGa                                >  2:1160839/1‑150 (MQ=17)                                                                                              aTTCCGTCTTGACCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATc                              <  1:204293/150‑1 (MQ=17)                                                                                                 ccGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAgg                           <  1:1261468/150‑1 (MQ=32)                                                                                                  aacagggcccatataatccgcaGATTTCGATTAGCCAGCCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAgg                                                                                 <  1:291394‑M1/76‑1 (MQ=255)                                                                                                  aacagggcccatataatccgcaGATTTCGATTAGCCAGCCTGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAgg                                                                                 >  2:291394‑M1/23‑98 (MQ=255)                                                                                                      ttGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTCTCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTa                                        <  1:756175/132‑1 (MQ=18)                                                                                                      ttGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTa                                        >  2:756175/1‑132 (MQ=33)                                                                                                      ttGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTAc                      >  1:326216/1‑150 (MQ=32)                                                                                                           ccAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACaga                                    >  1:1143547/1‑131 (MQ=33)                                                                                                           ccAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACaga                                    <  2:1143547/131‑1 (MQ=33)                                                                                                               cTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCaa              <  2:893681/149‑1 (MQ=32)                                                                                                               cTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCaa              >  1:893681/1‑149 (MQ=32)                                                                                                                 aaGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTAc                      >  1:670455/1‑139 (MQ=33)                                                                                                                 aaGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTAc                      <  2:670455/139‑1 (MQ=33)                                                                                                                    gCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACaga                                    >  1:993816/1‑122 (MQ=33)                                                                                                                    gCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACaga                                    <  2:993816/122‑1 (MQ=33)                                                                                                                    gCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAAc                  >  1:752507/1‑140 (MQ=33)                                                                                                                    gCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAAc                  >  1:752497/1‑140 (MQ=33)                                                                                                                    gCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAAc                  <  2:752497/140‑1 (MQ=33)                                                                                                                    gCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAAc                  <  2:752507/140‑1 (MQ=33)                                                                                                                       tGATTCCGATCAGCCGGA‑TGAGCGCGGCCTCTTGCGCTGGCTACCCCGCCTTGGGCGAAAGGGGGGGGCGATAAGGCTGGCTAA‑T‑CGAAATCTGGGGATTATAGGGGCCCTGTTACAGAGCGATCAGGTTTCCCAACGCAACCcgaacgg     <  2:1980424/150‑2 (MQ=11)                                                                                                                       tGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACcgaacga     >  1:191486/1‑150 (MQ=32)                                                                                                                       tGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCA‑‑CAGGTAAAGTGCGTAATCTGCGGGGTATATGGGCCCCGTTACAGAGCGATCAGGTTTACCAACGCAAACcgaacga     >  1:1571630/1‑150 (MQ=11)                                                                                                                        GATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCCTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACcgaacgaa    >  1:2046650‑M1/1‑150 (MQ=255)                                                                                                                          TTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACCGAACGaaaa  >  1:136303‑M1/1‑150 (MQ=255)                                                                                                                            |                                                                                                                                                       CCGATCAGCACAGCAGCGGAAACAAAATCAGATTGGGCAAGATGAGCAAGCGCGGTGACGGCTACATACGCAGCCTGATGATCCAGGGCGCGCATTCCGTCTTGAGCCAGCTAAGGCCTGATTCCGATCAGCCAGA‑TGATCGCCGCCTCTTGCGCTGGCTATCCCGCCTTGGGCGCAAGGAGGCGGCGATCAGGCTGGCTAA‑T‑CGAAATCTGCGGATTATATGGGCCCTGTTACAGAGCGATCAGGTTTACCAACGCAAACCGAACGAAAA  >  NC_002947/3968800‑3969070

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑