Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,376,442:1	+T	9.5%	intergenic (+17/‑131)	PP_2975 → / → PP_2976	insertion element ISR1 protein A3/transposase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,376,442	1	.	T	9.5%	152.7 / 9.2	42	intergenic (+17/‑131)	PP_2975/PP_2976	insertion element ISR1 protein A3/transposase
Reads supporting (aligned to +/- strand):  ref base . (22/16);  new base T (2/2);  total (24/18)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.54e-01

ATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACACCAAA  >  NC_002947/3376300‑3376590                                                                                                                                                |                                                                                                                                                      aTGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATg                                                                                                                                                 <  1:186205/149‑1 (MQ=255) aTGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATg                                                                                                                                                 <  1:27338/149‑1 (MQ=255)        catcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCgcag                                                                                                                                           <  2:157828/148‑1 (MQ=255)        catcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTC‑GCGCCGCTGAGATGgcttta                                                                                                                                           <  5:164781/148‑5 (MQ=255)          tcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGATCCGTCGGCTCAAGAAGATGTACGCCGAGGAGCTCCTCAAGGCCGAGATCATCCAGGAGGGCATGGCAATAAAGTGGTAAAGCCATCTCAGCGGCGA‑GAGATGGCGcagcag                                                                                                                                        >  1:127208/1‑149 (MQ=255)          tcatTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGTCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGcagcag                                                                                                                                        >  1:301186/1‑149 (MQ=255)                                   tGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGACTCAAGGCCGAGATAATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCACAGCCAGt                                                                                                               >  6:321063/1‑148 (MQ=255)                                          ggagAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTCAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAAt                                                                                                        >  7:263664/1‑148 (MQ=255)                                          ggagAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATATCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAAt                                                                                                        >  8:40101/1‑148 (MQ=255)                                           gagaACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAAt                                                                                                        >  2:26879/1‑147 (MQ=255)                                                 cGTCGGCGCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGc                                                                                                <  4:247268/149‑1 (MQ=255)                                                     ggCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTg                                                                                             <  7:40101/148‑1 (MQ=255)                                                            gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTgg                                                                                     >  7:150167/1‑149 (MQ=255)                                                            gaagaTGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTgg                                                                                     >  7:154262/1‑149 (MQ=255)                                                                   tACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGc                                                                              <  1:26879/149‑1 (MQ=255)                                                                      gCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAg                                                                               <  6:23406/145‑1 (MQ=255)                                                                      gCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAg                                                                               >  5:23406/1‑145 (MQ=255)                                                                        cGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGAc                                                                         <  2:70595/149‑1 (MQ=255)                                                                        cGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGAc                                                                         >  1:70595/1‑149 (MQ=255)                                                                        cGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGAc                                                                         >  7:153876/1‑149 (MQ=255)                                                                         gaggagCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACt                                                                        >  2:19670/1‑149 (MQ=255)                                                                            gagCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATc                                                                                 <  8:26196/137‑1 (MQ=255)                                                                            gagCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATc                                                                                 >  7:26196/1‑137 (MQ=255)                                                                             agCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAAc                                                                    <  8:150167/149‑1 (MQ=255)                                                                                  cTCAAGGCCGAGATCATCCAGGAGGCCATGGCAGAAAAGTGGTAAAGCCATCTCAGCAGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGccc                                                               >  4:124609/1‑149 (MQ=255)                                                                                       ggCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGt                                                          >  7:198446/1‑149 (MQ=255)                                                                                             gaTCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTc                                                                                           >  5:17166/1‑110 (MQ=255)                                                                                             gaTCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTc                                                                                           >  5:22989/1‑110 (MQ=255)                                                                                             gaTCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTc                                                                                           <  6:17166/110‑1 (MQ=255)                                                                                             gaTCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTc                                                                                           <  6:22989/110‑1 (MQ=255)                                                                                                 atcCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAgg                                                >  1:178737/1‑149 (MQ=255)                                                                                                 atcCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAgg                                                <  8:154262/149‑1 (MQ=255)                                                                                                 atcCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAgg                                                <  1:19670/149‑1 (MQ=255)                                                                                                    cAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTc                                             <  8:153876/149‑1 (MQ=255)                                                                                                               cccAAAAAAGTTGTAAAGCCATCACAGCTGCGC‑GAGATCCCGCAGCAGCC‑GGTTCGTTCAGGAAAAGCCAGTATCAAATTAACGTCCCTGTCGTTTGGTATCACCACGACTGAACCGCCCCGGGATACCCTGAGGCTCCACCCtat                                     >  8:117320/3‑144 (MQ=255)                                                                                                                        gTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAg                         <  2:301186/149‑1 (MQ=255)                                                                                                                                gCCATCTC‑GCGCCGCTGAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCatat                  >  1:19728/1‑148 (MQ=255)                                                                                                                                gCCATCTC‑GCGCCGCTGAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCatat                  >  8:165401/1‑148 (MQ=255)                                                                                                                                  cATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGag               <  8:263664/149‑1 (MQ=255)                                                                                                                                   aTCTCAGCGGCGC‑GAGATGGCGCAGCAGGCGGGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGag               >  1:43117/1‑149 (MQ=255)                                                                                                                                    tctcAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGagc              >  2:84308/1‑148 (MQ=255)                                                                                                                                      tcAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGagcaag           >  5:265890/1‑149 (MQ=255)                                                                                                                                              gc‑gAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACACCa    >  2:259224/1‑148 (MQ=255)                                                                                                                                              gc‑gAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGATTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCccacca    >  7:67174/1‑148 (MQ=255)                                                                                                                                               c‑gAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACACCaaa  <  8:198446/149‑1 (MQ=255)                                                                                                                                                |                                                                                                                                                      ATGGATGCATCATTGATGACCAGGCTGCGTGAACTGGAAGAGGAGAACCGTCGGCTCAAGAAGATGTACGCCGAGGAGCGCCTCAAGGCCGAGATCATCCAGGAGGCCATGGCAAAAAAGTGGTAAAGCCATCTCAGCGGCGC‑GAGATGGCGCAGCAGGC‑GGTTCGTTCAGGCAAAGCCAGTATCAAATTAGCGTGCCTGTCGTTTGGTATCAGCACGACTGAACCGCCCCGGGTTTCGCGGAGGCTCCACCCTTTGAGAGAATGGAGCCCATATGAGCAAGCACACCAAA  >  NC_002947/3376300‑3376590

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑