Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	ACB143	5,386,513	+AA	intergenic (‑522/+1129)	CJ019_05070 ← / ← nptII	hypothetical protein/neomycin phosphotransferase

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	ACB143	5,386,512	1	.	A	94.7%	59.8 / ‑2.7	19	intergenic (‑521/+1130)	CJ019_05070/nptII	hypothetical protein/neomycin phosphotransferase
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base A (8/10);  total (8/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.77e-01
*	ACB143	5,386,512	2	.	A	94.7%	60.5 / ‑2.7	19	intergenic (‑521/+1130)	CJ019_05070/nptII	hypothetical protein/neomycin phosphotransferase
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base A (8/10);  total (8/11)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.94e-01

TATTGATAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCCGTCGT‑‑‑CA‑GGA‑TC‑‑ATCCGGGCGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCTTGGGCTCC  >  ACB143/5386417‑5386609                                                                                                      ||                                                                                                  tATTGATAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGaa                                                              <  7:84131/137‑1 (MQ=255)       tAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCAc                                                        >  5:354002/1‑137 (MQ=255)            aaaaTTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTcc                                                   <  4:441254/137‑1 (MQ=255)              aaTTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCgg                                                 <  6:237848/137‑1 (MQ=255)              aaTTGATCCAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTGTACG‑GGACAA‑‑ACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCgg                                                 <  6:278733/137‑1 (MQ=255)              aaTTCATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCgg                                                 <  5:275831/137‑1 (MQ=255)                      caaTTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCtttt                                         <  8:101961/136‑1 (MQ=255)                                 tttAATACCCTAATATGACATCTCGGCCGGATTGTAGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCAGGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTg                              <  8:34957/137‑1 (MQ=255)                                            aaTATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAgg                   <  6:334671/137‑1 (MQ=255)                                            aaTATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAgg                   <  7:401381/137‑1 (MQ=255)                                            aaTATCACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAgg                   <  5:302790/137‑1 (MQ=255)                                              tatGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCAGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGc                 >  4:304534/1‑137 (MQ=255)                                               atGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGTGCTGCGGGTGCCAGGGCg                >  5:388394/1‑137 (MQ=255)                                                    atgcccgccggcTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACTGA‑CCAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGccc           <  2:442809/131‑1 (MQ=255)                                                     tctcGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCGGACGCTAGCAACGCATGAGAAAGGCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCt          >  5:121602/1‑137 (MQ=255)                                                      ctcGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGCTCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCtt         >  1:392942/1‑137 (MQ=255)                                                      ctcGGCCGGCTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCtt         >  5:178865/1‑137 (MQ=255)                                                         ggccggcTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCTTggg      >  4:57059/1‑137 (MQ=255)                                                             ggcTTGTCGACGACGGCGGTCTCAGTGGTG‑‑TACGGT‑ACAAACCCCGACGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTTCGCTGCGGGTGCCAGGGCGTGCCCTTGGGCTcc  >  5:58552/1‑137 (MQ=255)                                                                                                      ||                                                                                                  TATTGATAACAAAAATTGATCGAATTCTTTCATTTAAGACCCTAATATGACATCTCGGCCGGCTTGTCGACGACGGCGGTCTCCGTCGT‑‑‑CA‑GGA‑TC‑‑ATCCGGGCGCTAGCAACGCATGAGAAAGCCCCCGGAAGATCACCTTCCGGGGGCTTTTTTATTGCGCTGCGGGTGCCAGGGCGTGCCCTTGGGCTCC  >  ACB143/5386417‑5386609

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑