Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP002416	665,962	T→C	intergenic (+88/‑283)	Clo1313_0602 → / → Clo1313_0603	transposase mutator type/YD repeat protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP002416	665,962	0	T	C	95.5%	59.3 / ‑3.4	22	intergenic (+88/‑283)	Clo1313_0602/Clo1313_0603	transposase mutator type/YD repeat protein
Reads supporting (aligned to +/- strand):  ref base T (0/1);  new base C (8/13);  total (8/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.55e-01

TCTTTGTCAAATTTTTCTTTTGTAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACATATA  >  CP002416/665940‑666108                       |                                                                                                                                                   tcTTTGTCAAATTTTTCTTTTGTAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCAc                    <  1:1443058/151‑1 (MQ=11) tcTTTGTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCAc                    >  1:3228813/1‑151 (MQ=11)  cTTTGTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACt                   <  1:2807455/151‑1 (MQ=14)  cTTTGTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACt                   <  1:3182574/151‑1 (MQ=14)   tttGTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTg                  <  1:549684/151‑1 (MQ=14)   tttGTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTg                  <  1:203794/151‑1 (MQ=14)   tttGTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTg                  >  1:2920235/1‑151 (MQ=14)    ttGTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGa                 <  1:484951/151‑1 (MQ=17)      gTCAAATTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGaaa               >  1:744064/1‑151 (MQ=18)         aaaTTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGc            >  1:2546929/1‑151 (MQ=25)          aaTTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCa           <  1:2702398/151‑1 (MQ=37)          aaTTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCa           <  1:45274/151‑1 (MQ=37)           aTTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCaa          <  1:2916227/151‑1 (MQ=38)           aTTTTTCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCaa          <  1:2534417/151‑1 (MQ=38)             ttttCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCaaaa        >  1:104189/1‑151 (MQ=255)             ttttCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCaaaa        <  1:1825784/151‑1 (MQ=255)               ttCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAATCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACa      <  1:2738409/151‑1 (MQ=255)               ttCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACa      <  1:2726790/151‑1 (MQ=255)                tCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACat     <  1:621176/151‑1 (MQ=255)                tCTTTTGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACat     >  1:2102586/1‑151 (MQ=255)                  ttttGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACatat   >  1:407235/1‑151 (MQ=255)                   tttGCAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACatata  >  1:2798846/1‑151 (MQ=255)                       |                                                                                                                                                   TCTTTGTCAAATTTTTCTTTTGTAAGAATTTCTTATCAGAAATTCTTTTGAATCTATAAAATTTGACAAAGCAGACTTTCGAGTCTTAAAATATATTTAAATACTAACATAGAAGGAAAATTAGTTTACACAAAAATATTTACACTGCCACTGAAAGGCAAAACATATA  >  CP002416/665940‑666108

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 38 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑