Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	684,503:1	+A	70.5%	intergenic (‑34/+296)	insH1 ← / ← lnt	IS5 transposase and trans‑activator/apolipoprotein N‑acyltransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	684,503	1	.	A	70.5%	115.7 / 47.9	44	intergenic (‑34/+296)	insH1/lnt	IS5 transposase and trans‑activator/apolipoprotein N‑acyltransferase
Reads supporting (aligned to +/- strand):  ref base . (8/5);  new base A (15/16);  total (23/21)
Fisher's exact test for biased strand distribution p-value = 5.18e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.27e-01

TCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCGCTGGATTACTGTGGTGCAACTAGGTTGTAC  >  CP009273/684374‑684650                                                                                                                                   |                                                                                                                                                    tCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGc                                                                                                                                  >  2:96044/1‑150 (MQ=255)       cTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGTTGACTCATGATGAACCCTGTTCTATGGCCCCCGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATg                                                                                                                            >  2:900215/1‑149 (MQ=255)        tGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATg                                                                                                                            >  2:343522/1‑149 (MQ=255)            ggCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAg                                                                                                                       <  2:622907/150‑1 (MQ=255)              cgcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGat                                                                                                                     <  1:934322/150‑1 (MQ=255)              cgcTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGat                                                                                                                     <  2:157646/150‑1 (MQ=255)                cTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGatat                                                                                                                   <  1:893112/150‑1 (MQ=255)                    ctgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTg                                                                                                              >  1:437584/1‑150 (MQ=255)                     tgctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAATTGTAAAGATATTGCTg                                                                                                              >  1:360299/1‑150 (MQ=255)                       ctgAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTg                                                                                                              <  2:972687/148‑1 (MQ=255)                           aTTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTAt                                                                                                        <  1:290709/150‑1 (MQ=255)                               aCTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTAttgttt                                                                                                   <  2:265062/150‑1 (MQ=255)                                  gTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATtgtttgtt                                                                                                >  1:427306/1‑150 (MQ=255)                                   tCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATtgtttgtt                                                                                                <  2:383131/149‑1 (MQ=255)                                      gCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGttttt                                                                                             >  2:528784/1‑150 (MQ=255)                                        gAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGc                                                                                           >  2:661598/1‑150 (MQ=255)                                           ggTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGc                                                                                           >  2:253019/1‑146 (MQ=255)                                            gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGAt                                                                                      <  1:900215/150‑1 (MQ=255)                                            gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGAt                                                                                      >  2:867927/1‑150 (MQ=255)                                            gTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGAt                                                                                      <  1:571781/150‑1 (MQ=255)                                                    atgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGcgccg                                                                                >  2:750905/1‑149 (MQ=255)                                                     tgaCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCa                                                                              <  1:688481/150‑1 (MQ=255)                                                       aCTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCAcc                                                                            <  2:539487/150‑1 (MQ=255)                                                        cTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCa                                                                           <  2:819646/150‑1 (MQ=255)                                                          cATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCAtt                                                                         >  1:352854/1‑150 (MQ=255)                                                          cATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCAtt                                                                         >  1:555852/1‑150 (MQ=255)                                                               tgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGaa                                                                    <  1:638756/150‑1 (MQ=255)                                                               tgaACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAg                                                                   <  2:575813/150‑1 (MQ=255)                                                                 aaCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGc                                                                  <  1:96044/150‑1 (MQ=255)                                                                  aCCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGc                                                                  >  1:624476/1‑149 (MQ=255)                                                                   cccTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCaa                                                                >  2:168567/1‑149 (MQ=255)                                                                      tGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAAt                                                             >  1:257237/1‑150 (MQ=255)                                                                             tGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCtt                                                         <  1:853839/147‑1 (MQ=255)                                                                             tGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTaa                                                       >  2:18264/1‑149 (MQ=255)                                                                                      aTGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCtt                                            >  1:77470/1‑150 (MQ=255)                                                                                        gACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCttt                                           >  2:405330/1‑150 (MQ=255)                                                                                         aCAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCttt                                           >  2:794332/1‑149 (MQ=255)                                                                                             aCATGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTg                                      <  1:522398/150‑1 (MQ=255)                                                                                                tGATCTCATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTa                                   <  2:555852/150‑1 (MQ=255)                                                                                                   tctcATATCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCg                                >  2:964277/1‑150 (MQ=255)                                                                                                         atCAGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCGCTGGAt                          >  2:473523/1‑150 (MQ=255)                                                                                                            aGGGACTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCGCTGGATTa                        <  2:917328/149‑1 (MQ=255)                                                                                                                aCTTGTTCGCACCTTCCTTAAGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCGCTGGATTACtgtg                   <  2:302097/150‑1 (MQ=255)                                                                                                                       cGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCGCTGGATTACTGTGGTGCAAc            >  1:225556/1‑149 (MQ=255)                                                                                                                               cctt‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTG‑TTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCGCTGGATTACTGTGGTGCAACTAGGTTGTAc  >  2:821556/1‑150 (MQ=255)                                                                                                                                   |                                                                                                                                                    TCTGGTCTGACGGCGCTTACTGCTGAATTCACTGTCGGCGAAGGTAAGTTGATGACTCATGATGAACCCTGTTCTATGGCTCCAGATGACAAACATGATCTCATATCAGGGACTTGTTCGCACCTTCCTT‑AGGTAACATTTAGTTTGGCTAAATGTAAAGATATTGCTGTTTTATTGTTTGTTTTTGCGAGATGCGCCGCACCATTCCGAAGCAAAATTCTTAAAATGCACTCTTTTAGTGCTACCGCTGGATTACTGTGGTGCAACTAGGTTGTAC  >  CP009273/684374‑684650

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 30 ≤ ATCG/ATCG < 34 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑