Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,517,508	G→T	V40V (GTG→GTT)	ortT →	orphan toxin OrtT

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,517,508	0	G	T	96.5%	96.1 / ‑6.4	29	V40V (GTG→GTT)	ortT	orphan toxin OrtT
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base T (18/10);  total (19/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.98e-01

GATAAGGGCAAGTTGCTGTTTGATGATTTTTTCTCAAACTGGTGAAAAAACTTGATGCACGTCAAAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAATTATTAATCGCCCTGAGCGATGACGCGGA  >  NC_000913/1517273‑1517751                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                    gATAAGGGCAAGTTGCTGTTTGATGATTTTTTCTCAAACTGGTGAAAAAACTTGATGCACGTCAAAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCg                                                                                                                                                                                                                                      >  2:123271/1‑251 (MQ=255)      gggCAAGTTGCTGTTTGATGATTTTTTCTCAAACTGGTGAAAAAACTTGATGCACGTCAAAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGa                                                                                                                                                                                                                                  <  2:317999/250‑1 (MQ=255)      gggCAAGTTGCTGTTTGATGATTTTTTCTCAAACTGGTGAAAAAACTTGATGCACGTCAAAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGa                                                                                                                                                                                                                                  >  1:317999/1‑250 (MQ=255)                                     aaCTGGTGAAAAAACTTGATGCACGTCAAAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGttt                                                                                                                                                                                                  >  1:22948/1‑251 (MQ=255)                                                          cACGTCAAAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTg                                                                                                                                                                             >  1:350520/1‑251 (MQ=255)                                                                       gACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTAGACGGCACCACGc                                                                                                                                                                 >  1:9398/1‑250 (MQ=255)                                                                           cATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAgcct                                                                                                                                                            >  2:49194/1‑248 (MQ=255)                                                                           cATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACt                                                                                                                                                            <  2:255182/251‑1 (MQ=255)                                                                                     cgcgTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGCCTTATATCAttt                                                                                                                                                  >  2:5317/1‑251 (MQ=255)                                                                                        gTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTAGCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCGCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCAATGGCTTGACGGCACCACGCAGACTTATATCATTTGGa                                                                                                                                               <  2:294296/251‑1 (MQ=255)                                                                                             aTTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAAt                                                                                                                                          <  2:47227/251‑1 (MQ=255)                                                                                                  tCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGAt                                                                                                                                      >  1:316596/1‑250 (MQ=255)                                                                                                     ggctggACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAAt                                                                                                                                  <  1:282020/251‑1 (MQ=255)                                                                                                             gCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTcaca                                                                                                                            >  1:176918/1‑249 (MQ=255)                                                                                                                       gTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAgg                                                                                                                 >  1:95532/1‑250 (MQ=255)                                                                                                                                           ttGTTTTTTATGCGGGTATGGCAGCAATCGCATTTCTTATAACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCCCCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTgg                                                                                             >  2:129436/1‑250 (MQ=255)                                                                                                                                                   tATGCGGTTATGGCAGCAATAGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGATTTAAATCTTACTCGCTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAAACGATAAATTTCACAAGTGGCTAAGGAGAAAGCATGTCGCATCTGGATGAGGTc                                                                                     >  2:379517/1‑250 (MQ=255)                                                                                                                                                              ggCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGt                                                                          <  1:28234/250‑1 (MQ=255)                                                                                                                                                                       cGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCcgc                                                                 <  2:298257/250‑1 (MQ=255)                                                                                                                                                                                            tctttctCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACCGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGcc                                           >  2:341983/1‑251 (MQ=255)                                                                                                                                                                                             ctttctCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGccc                                          >  2:332978/1‑251 (MQ=255)                                                                                                                                                                                                         aaGAAACGTATCCGTTTCTTAAGCGCCTTTCTTGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAat                              <  2:316596/251‑1 (MQ=255)                                                                                                                                                                                                         aaGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGaa                               <  1:161926/250‑1 (MQ=255)                                                                                                                                                                                                            aaaCGCATCCGTTTCTTCAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAattat                           >  2:281590/1‑251 (MQ=255)                                                                                                                                                                                                                  aTCCGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAATTATTAATCg                     >  1:294824/1‑251 (MQ=255)                                                                                                                                                                                                                     cGTTTCTTAAGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAATTATTAATCGccc                  >  2:77577/1‑251 (MQ=255)                                                                                                                                                                                                                             aaGCGCCTTTCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAATTATTAATCGCCCTGAGCGAt          <  1:77577/251‑1 (MQ=255)                                                                                                                                                                                                                                     ttCTGGTTGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAATTATTAATCGCCCTGAGCGATGACGCgg   >  1:169172/1‑250 (MQ=255)                                                                                                                                                                                                                                     ttCTGGTGGGGGCAACATGGCCGATGAGTTTCTGGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGAAGAATCGATAAATTTAACAAGAGGCTAAGGAGAAAGTATGTTGCATCTGGCTGAAGTCATCGCGCGCGTGGATGCCGCGATTAATGCGAGCGTCATTGCCCATATGAGCGAATTGTTAATCGCCCTGAGCGAtatcgcggt  >  2:246991/1‑243 (MQ=255)                                                                                                                                                                                                                                            |                                                                                                                                                                                                                                                    GATAAGGGCAAGTTGCTGTTTGATGATTTTTTCTCAAACTGGTGAAAAAACTTGATGCACGTCAAAAAATGACGCATATTTGCGCGCGTTTTATTCATCTGGCTGGACGCCCGTACATGTCTCTCTATCAACACATGCTTGTTTTTTATGCGGTTATGGCAGCAATCGCATTTCTTATCACCTGGTTTCTTTCTCACGATAAGAAACGCATCCGTTTCTTAAGCGCCTTTCTGGTGGGGGCAACATGGCCGATGAGTTTCCCGGTGGCGCTGTTGTTTTCACTGTTTTAAATCTTACTCACTGGCTTGACGGCACCACGCAGACTTATATCATTTGGATGAATCGATAAATTTCACAAGTGGCTAAGGAGAAAGTATGTCGCATCTGGATGAAGTCATCGCGCGCGTGGATGCCGCGATTGAAGAGAGCGTCATTGCCCATATGAACGAATTATTAATCGCCCTGAGCGATGACGCGGA  >  NC_000913/1517273‑1517751

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 18 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑