Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,412,897	G→A	L113L (CTC→CTT)	intR ←	putative integrase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,412,897	0	G	A	96.5%	95.4 / ‑3.7	29	L113L (CTC→CTT)	intR	putative integrase
Reads supporting (aligned to +/- strand):  ref base G (1/0);  new base A (12/16);  total (13/16)
Fisher's exact test for biased strand distribution p-value = 4.48e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.01e-01

GTAATTTTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATC  >  NC_000913/1412659‑1413134                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                              gTAATTTTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTa                                                                                                                                                                                                                                     <  2:338923/249‑1 (MQ=255)   aaTTTTTTTACTCCTTCAAATGGTTTGGTTGATATAAAGCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATtg                                                                                                                                                                                                                                 <  1:183719/251‑1 (MQ=255)         tttACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGAtt                                                                                                                                                                                                                            <  1:248151/250‑1 (MQ=255)           tACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTc                                                                                                                                                                                                                          <  1:370405/250‑1 (MQ=255)            aCTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGt                                                                                                                                                                                                                        <  1:173580/251‑1 (MQ=255)                cTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTttc                                                                                                                                                                                                                    >  1:426765/1‑251 (MQ=255)                   cAAATGGTTTGGTTGATATATATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCTCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTttctt                                                                                                                                                                                                                  <  1:459756/250‑1 (MQ=255)                                        aTCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGCTTTCGTTTTCTTCATTGTGTTTGTTGTTAActct                                                                                                                                                                                            >  1:331007/1‑251 (MQ=255)                                        aTCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAActct                                                                                                                                                                                            <  1:137508/251‑1 (MQ=255)                                                    aagCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCCTGCAGCAGTTCATTCCGGTCGTTTAAGATATCGCTATACCGACTATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTAATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAAtt                                                                                                                                                                                >  2:427091/3‑251 (MQ=255)                                                      gCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGCGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAAtttt                                                                                                                                                                              <  1:379443/251‑1 (MQ=255)                                                         aaaCTCAACAGCGAACAGAGCAGGGCGATATAGGTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGt                                                                                                                                                                           <  1:94214/251‑1 (MQ=255)                                                            cGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTcc                                                                                                                                                                         >  1:457246/1‑250 (MQ=255)                                                                     gAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATcac                                                                                                                                                                >  1:433737/1‑250 (MQ=255)                                                                           agCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACACATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGctc                                                                                                                                                         >  2:135171/1‑251 (MQ=255)                                                                                    atatAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGt                                                                                                                                                <  1:142964/251‑1 (MQ=255)                                                                                                         aCGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTCAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTACTTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCAc                                                                                                                           >  2:570900/1‑251 (MQ=255)                                                                                                         aCGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCAc                                                                                                                           >  2:568570/1‑251 (MQ=255)                                                                                                                        ttgttgGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAg                                                                                                             <  1:135171/250‑1 (MQ=255)                                                                                                                         tgttgGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCTCCATTTTTGCCCCAGTg                                                                                                           >  1:180650/1‑251 (MQ=255)                                                                                                                           ttgGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCTCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTCTTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGtcat                                                                                                         >  2:392920/1‑248 (MQ=255)                                                                                                                                           ccAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACg                                                                                          <  1:521796/250‑1 (MQ=255)                                                                                                                                                      gTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTc                                                                              <  2:457246/251‑1 (MQ=255)                                                                                                                                                            ccATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCaaa                                                                           <  1:124082/248‑1 (MQ=255)                                                                                                                                                              aTGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAATTACTCAAATTCAc                                                                      >  2:528292/1‑251 (MQ=255)                                                                                                                                                                gcagcaGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCAcc                                                                     <  1:500224/250‑1 (MQ=255)                                                                                                                                                                                                                  ctCGGGGTACTTTCACAAATTATTATTCTACGTGTTTTTAATTGCGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGTCTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATAAGCGCTCTTAAATTTCCGGCCTTTTTAat                  >  2:89099/2‑251 (MQ=255)                                                                                                                                                                                                                               cacaAATTATTATTCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGt      >  1:381518/1‑250 (MQ=255)                                                                                                                                                                                                                                  aaaTTATTAATCTAAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAAtc  <  2:202842/251‑1 (MQ=255)                                                                                                                                                                                                                                               |                                                                                                                                                                                                                                              GTAATTTTTTTACTCCTTCAAATGGTTTGGTTGATATAAATCCCGACTGATACGCAAAACGCAACAGCGAACAGAGCAGGGCGATATAGTTATCAACTGTGCGCACGGTTCTTCCTTTTTTGTTGGATCTTGGATTATCCAGGTAAAGCGTTTCTCCATGCAGCAGTTCATTCCGGTAGTTTAAGATATCGCTATAACGAATATGTGATATCGGGGTACTTTCACAAATTATTATTCTGAGTGTTTTTAATTGTGATTTCGTTTTCTTCATTGTGTTTGTTGTTAACTCTGTCTCTTTAATTTTTGTCCAGATATCACAAAGCTCTCCGAACGTTTTTATGACTCTCGTTGTCACCATTTTTGCCCCAGTGCTGGACTGGGGAAAACGTCTTAAATACTCAAATTCACCGGAGTTTATTTCATGAACTATCAGCGCTCTTAAATTTCCGGCCTTTTTAATATTACTGTTTGTAATC  >  NC_000913/1412659‑1413134

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑