Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_002947	3,379,185	A→T	8.1%	S322T (TCT→ACT)	tnpS ←	cointegrate resolution protein S

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_002947	3,379,185	0	A	T	8.1%	139.6 / 3.2	49	S322T (TCT→ACT)	tnpS	cointegrate resolution protein S
Reads supporting (aligned to +/- strand):  ref base A (22/23);  new base T (2/2);  total (24/25)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.78e-01

AAGGGATTTTATAATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGTCATCAAGGCCTTG  >  NC_002947/3379040‑3379324                                                                                                                                                  |                                                                                                                                            aaGGGATTTTATAATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGc                                                                                                                                          <  1:318928/149‑1 (MQ=255)  aGGGATTTTATAATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCt                                                                                                                                         <  4:94986/149‑1 (MQ=255)       ttttATAATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAg                                                                                                                                    <  3:200056/149‑1 (MQ=255)          tataATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGtt                                                                                                                                  >  5:202375/1‑148 (MQ=255)           ataATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGACGATATTAATGAGAAGCt                                                                                                                                         <  4:185541/140‑1 (MQ=255)           ataATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGACGATATTAATGAGAAGCt                                                                                                                                         >  3:185541/1‑140 (MQ=255)            taATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGAc                                                                                                                               <  6:54534/149‑1 (MQ=255)                    ctATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAgg                                                                                                                        <  4:2682/148‑1 (MQ=255)                     tataATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTAAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTACATGTTGCGCCATCGTACAAGGGGTGACACGATAATAAAGAGAAGCTGAAAGTTGACCCAAAGGGc                                                                                                                      >  8:255921/1‑149 (MQ=255)                        aaTTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGc                                                                                                                      >  7:92999/1‑146 (MQ=255)                         aTTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAg                                                                                                                   >  2:130045/1‑148 (MQ=255)                          ttAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCACTGGGGTGTGCCGTAAGTAATGATAAGCTGAAAGTTGACCCAAAGTGCCCGCa                                                                                                                 >  4:197288/1‑149 (MQ=255)                                            taAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGt                                                                                               >  5:146704/1‑149 (MQ=255)                                              aaGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGtt                                                                                              <  3:137219/148‑1 (MQ=255)                                                gCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAg                                                                                                                         >  5:67741/1‑119 (MQ=255)                                                gCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAg                                                                                                                         <  6:67741/119‑1 (MQ=255)                                                gCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAg                                                                                           >  3:59472/1‑149 (MQ=255)                                                    aTTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCCTGGTCCCTGGGGTGTGGCGATATTAATGTGAAGCTGAAAGGTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCt                                                                                         <  3:197288/147‑1 (MQ=255)                                                    aTTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAg                                                                                                                                           >  3:248182/1‑97 (MQ=255)                                                    aTTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAg                                                                                                                                           <  4:248182/97‑1 (MQ=255)                                                    aTTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCt                                                                                         <  5:40645/147‑1 (MQ=255)                                                    aTTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTg                                                                                        >  2:166525/1‑148 (MQ=255)                                                       cTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCaa                                                                                     <  1:130045/148‑1 (MQ=255)                                                            gctgCTCAACTGCCTGTATGTGTTGAGAGAGACAGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCAGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGTACAGTTTTAGCTGCAAGgccgc                                                                               <  7:117815/146‑1 (MQ=255)                                                                        ccTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATg                                                                    <  6:128881/148‑1 (MQ=255)                                                                         cTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGATTGAAGCTAATGGACTGGTTTTGCTGCATGGCCGCAAATggtattggg                                                                  >  3:295055/1‑142 (MQ=255)                                                                           gTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGTAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCgg                                                                >  8:34697/1‑149 (MQ=255)                                                                           gTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGTAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCgg                                                                >  8:73656/1‑149 (MQ=255)                                                                             aTGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCgggg                                                              >  6:16702/1‑149 (MQ=255)                                                                                 gtTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGa                                                          >  4:104321/1‑149 (MQ=255)                                                                                 gtTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGa                                                          >  2:284326/1‑149 (MQ=255)                                                                                    gagagaGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGAGCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATg                                                        <  6:202375/148‑1 (MQ=255)                                                                                        gagCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAgc                                                    <  4:59472/148‑1 (MQ=255)                                                                                            ccGATTACACTTCATGTTGCGCCATCGTCCCTGCGGTGTGCCGAAATTAATGAGAAGCTGAAACTTGACCCCAAGGGCCAGCATGAAGCTCAAGGACAGGATTACCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATg                                               >  7:46927/1‑149 (MQ=255)                                                                                             cGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATgg                                              <  1:166525/149‑1 (MQ=255)                                                                                              gATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATgg                                              >  7:30122/1‑148 (MQ=255)                                                                                                     cTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTa                                                      >  2:208523/1‑133 (MQ=255)                                                                                                     cTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTa                                                      <  1:208523/133‑1 (MQ=255)                                                                                                     cTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTg                                      <  1:284326/149‑1 (MQ=255)                                                                                                        cATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGAt                                    <  8:92999/148‑1 (MQ=255)                                                                                                                gcCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTc                             >  1:214722/1‑147 (MQ=255)                                                                                                                      gTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACACAAAGCGCCAGCATGAAGCTAAAGGACAGTTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCTCATGGCAGACTTGATGTCTTTCCAGCCTa                      >  1:172227/1‑148 (MQ=255)                                                                                                                             gggTGTTCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGtc              <  7:255921/149‑1 (MQ=255)                                                                                                                             gggTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAgg                <  2:214722/147‑1 (MQ=255)                                                                                                                                      gATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGACGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGTCATCAAGGcc     >  6:278550/1‑149 (MQ=255)                                                                                                                                          ttAATGAGTAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGTCATCAAGGCCTTg  <  7:34697/148‑1 (MQ=255)                                                                                                                                          ttAATGAGTAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGTCATCAAGGCCTTg  <  7:73656/148‑1 (MQ=255)                                                                                                                                          ttAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGTCATCAAGGCCTTg  <  8:30122/148‑1 (MQ=255)                                                                                                                                            aaTGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGTCATCAAGGCCtt   >  8:128296/1‑145 (MQ=255)                                                                                                                                                  |                                                                                                                                            AAGGGATTTTATAATCGCTCTATAATTAAACTATAAAGATCTATAAAGCTCATTCTAGAGCGGCTCAACTGCCTGTATGTGTTGAGAGAGCCCGATTACACTTCATGTTGCGCCATCGTCCCTGGGGTGTGCCGATATTAATGAGAAGCTGAAAGTTGACCCAAAGGGCCAGCATGAAGCTCAAGGACAGGTTTAGCTGCAAGGCCGCCAAAGGATATGGCGGGGTCGATGTAGCGCATGGCAGACTTGATGTCTTTCCAGCCTACATAGGTCATCAAGGCCTTG  >  NC_002947/3379040‑3379324

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: ‑