Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	391,739	C→T	*289* (TAG→TAA)	insF1 ←	IS3 transposase B

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	391,739	0	C	T	98.4%	169.2 / ‑4.4	62	*289* (TAG→TAA)	insF1	IS3 transposase B
Reads supporting (aligned to +/- strand):  ref base C (1/0);  new base T (33/28);  total (34/28)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 8.09e-01

CTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGT‑GGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC  >  NC_000913/391605‑391845                                                                                                                                        |                                                                                                           cttcGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTaa                                                                                                         >  2:152447/1‑139 (MQ=255)         aaCATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGtt                                                                                                 >  2:241828/1‑139 (MQ=255)                   aaGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCa                                                                                       >  1:1411145/1‑139 (MQ=255)                     gATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     <  1:202743/139‑1 (MQ=255)                     gATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     >  2:258345/1‑139 (MQ=255)                                  aTACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTACTATGGCAACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTg                                                                        >  1:1012728/1‑139 (MQ=25)                                    aCCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAg                                                                      >  2:717691/1‑139 (MQ=255)                                    aCCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAg                                                                      >  2:3205/1‑139 (MQ=255)                                       gATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgcc                                                                   <  1:1061859/139‑1 (MQ=255)                                                    ttAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGGTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACtg                                                      >  1:302826/1‑139 (MQ=255)                                                    ttAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACtg                                                      >  2:729574/1‑139 (MQ=255)                                                    ttAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACtg                                                      >  1:806829/1‑139 (MQ=255)                                                    ttAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACtg                                                      >  1:53654/1‑139 (MQ=255)                                                     tAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACtgt                                                     >  1:274236/1‑139 (MQ=255)                                                       aCTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGt                                                                                 <  1:359891/109‑1 (MQ=255)                                                       aCTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGt                                                                                 >  2:359891/1‑109 (MQ=255)                                                          ccTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAg                                                                      >  2:1047182/1‑117 (MQ=255)                                                          ccTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAg                                                                      <  1:1047182/117‑1 (MQ=255)                                                           cTACAGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgccgcc                                               <  1:729574/139‑1 (MQ=255)                                                               aGTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCa                                           <  1:258345/139‑1 (MQ=255)                                                                gTACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCCTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCAc                                          <  2:410437/139‑1 (MQ=255)                                                                 tACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgccgc                                                                 >  1:1179363/1‑115 (MQ=255)                                                                 tACTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgccgc                                                                 <  2:1179363/115‑1 (MQ=255)                                                                   cTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTGCGGACTGAGGCCGCCACACCAACTGTgccg                                                 >  2:890428/1‑129 (MQ=255)                                                                   cTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTgccg                                                 <  1:890428/129‑1 (MQ=255)                                                                   cTGTTGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGa                                       >  2:528366/1‑139 (MQ=255)                                                                    ggTTGCGTTGACCGAAGCGACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGGGACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAATTGTGCCGCCGCCACCGAt                                      <  1:15653/138‑1 (MQ=17)                                                                      ttGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTg                                    >  1:320404/1‑139 (MQ=255)                                                                      ttGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTg                                    >  1:591691/1‑139 (MQ=255)                                                                      ttGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTg                                    >  1:1380815/1‑139 (MQ=255)                                                                      ttGCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTg                                    >  2:1452067/1‑139 (MQ=255)                                                                        gCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     <  1:1026544/88‑1 (MQ=18)                                                                        gCGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     >  2:1026544/1‑88 (MQ=18)                                                                         cGTTGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTaa                                 >  2:711777/1‑139 (MQ=255)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACTCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATc                               >  2:809240/1‑139 (MQ=255)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     >  2:1348103/1‑85 (MQ=18)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCaaa                                                                                     <  1:1348103/85‑1 (MQ=18)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgccgc                                                                 >  2:1042594/1‑105 (MQ=255)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATc                               <  1:241828/139‑1 (MQ=255)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGACGCCACACCAACTGTGCCGCCGCCACCGATTGTAAt                                >  2:153045/1‑138 (MQ=255)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGACGCCACACCAACTGTGCCGCCGCCACCGATTGTAAt                                <  1:153045/138‑1 (MQ=255)                                                                           ttGACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGATTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGgccgc                                                                 <  1:1042594/105‑1 (MQ=17)                                                                             gACCGAATCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGGGCCGCCGCCACCGATTGTAATcac                             >  2:821366/1‑139 (MQ=255)                                                                                   aTCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa                       <  2:806829/139‑1 (MQ=255)                                                                                   aTCTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa                       <  2:53654/139‑1 (MQ=255)                                                                                     cTACTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGata                     <  1:717691/139‑1 (MQ=255)                                                                                       aCTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAAGTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGAtata                   <  1:1271912/139‑1 (MQ=255)                                                                                        cTGGGTGGGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATaa                  <  2:1411145/139‑1 (MQ=255)                                                                                            gt‑gggGGGCTGATTGATCCTACCCACGTAATATGGACAAAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACC‑ACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAac            >  2:292888/1‑139 (MQ=255)                                                                                               ggggggCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAaca           <  1:1425907/139‑1 (MQ=37)                                                                                                gggggCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTg                                    >  2:912354/1‑113 (MQ=37)                                                                                                gggggCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTg                                    <  1:912354/113‑1 (MQ=37)                                                                                                gggggCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa                       >  2:622039/1‑126 (MQ=37)                                                                                                gggggCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGa                       <  1:622039/126‑1 (MQ=25)                                                                                                  gggCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATc                               >  2:719699/1‑116 (MQ=25)                                                                                                  gggCTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATc                               <  1:719699/116‑1 (MQ=25)                                                                                                     cTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACAtt                          <  1:146672/118‑1 (MQ=18)                                                                                                     cTGATTGATCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACAtt                          >  2:146672/1‑118 (MQ=17)                                                                                                       gattgatCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGcc   >  2:815898/1‑139 (MQ=14)                                                                                                        attgatCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGccc  <  2:465422/139‑1 (MQ=11)                                                                                                        attgatCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGccc  <  2:274236/139‑1 (MQ=11)                                                                                                        attgatCCTACCCACGTAATATGGACACAGGCTTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGccc  <  1:711777/139‑1 (MQ=11)                                                                                                                                        |                                                                                                           CTTCGCTGAACATTGGTGAAGATGGCTACGTTGATACCGATCATCTGACTATTAACTCCTACAGTACTGTTGCGTTGACCGAATCTACTGGGT‑GGGGGGCTGATTGATCCTACCCACGTAATATGGACACAGGCCTAAGCGAGGTTCTTGTTTTCAAATTGTTCCGGACTGAGGCCGCCACACCAACTGTGCCGCCGCCACCGATTGTAATCACATTCGATATAATTAAACACCGTTGCCC  >  NC_000913/391605‑391845

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑