Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,958,806	C→T	N279N (AAC→AAT)	ilvC →	ketol‑acid reductoisomerase (NADP(+))

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,958,806	0	C	T	95.0%	49.7 / ‑3.3	20	N279N (AAC→AAT)	ilvC	ketol‑acid reductoisomerase (NADP(+))
Reads supporting (aligned to +/- strand):  ref base C (0/1);  new base T (11/8);  total (11/9)
Fisher's exact test for biased strand distribution p-value = 4.50e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 5.91e-01

GCGGGTGTGCTGGAATCGTCCTTCGTTGCGGAAGTGAAATCTGACCTGATGGGCGAGCAAACCATCCTGTGCGGTATGTTGCAGGCTGGCTCTCTGCTGTGCTTCGACAAGCTGGTGGAAGAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAACCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGGACGACATCATCTCCGGCGAATTCTCTTCCGGTATGATGGCGGACTGGGCCAACGATGATAAGAAACTGCTGACCTGGCGTGAAGAGACCGGCAAAACCGCGTTTGAAACCG  >  NC_000913/3958576‑3958993                                                                                                                                                                                                                                       |                                                                                                                                                                                            gCGGGTGTGCTGGAATCGTCCTTCGTTGCGGTAGTGAAATCTGACCTGATGGGCGAGCAAACCATCCTGTGCGGTATGTTGCATGCTGGCTCTCTGCTGTGCTTCGACAAGCTGGTGGAATAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCTCCGAATCACTTAAACAGGGCGGCATCACCCTTATTATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTa                                                                                                                                                                         <  1:208081/251‑1 (MQ=255)                                                                        cGGTATGTTGCAGGCTGGCTCTCTGCTGTGCTTCGACAAGCTGGTGGAAGAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCtn                                                                                                                                                              <  1:301622/191‑2 (MQ=255)                                                                            aTGTTGCAGGCTGGCTCTCTGCTGTGCTTCGACAAGCTGGTGGAAGAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGa                                                                                                                          >  1:238580/1‑223 (MQ=255)                                                                                         gctCTCTGCTGTGCTTCGACAAGCTGGTGGAAGAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGGACGACATCATCTCCGGCGAATTCTCTTCCGGt                                                                                 >  1:88580/1‑251 (MQ=255)                                                                                               tgctgTGCTAAGACAAGCTGGAGGAAGAAGGTACCGCTCCAGCATACGCAGAAAAACTGATTAAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGGACGACATCATCTACGGCGAATTCTCTTCCGGGatgatg                                                                           >  1:118091/1‑251 (MQ=255)                                                                                                gctgTGCTTCGACAAGCTGGTGGAAGAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGgacgan                                                                                                            <  1:124450/217‑2 (MQ=255)                                                                                                        tCGACAAGCTTGTGGAAGAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGATTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCGCCCTGATGATGGACCGTCTCTCTAACCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAGCATATGGACGACATCATCTCCGGCGAAGTCTCTTCCGGTATGATGGCGGACTg                                                                   <  1:494320/250‑1 (MQ=255)                                                                                                                           agGTACCGATCCAGCATACGCCGAACAACTGATAAAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGc                                                                                                                                                                                        >  1:136503/1‑114 (MQ=255)                                                                                                                             gTACCGATCCCGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGCCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCa                                                                                                                                            >  1:140020/1‑156 (MQ=255)                                                                                                                               nccGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGGACGACATCATCTCCGGCGAATTCTCTTCCGGTATGATGGCGGACTGGGCCAACGATGATAAGAAActgct                                           >  1:298361/2‑251 (MQ=255)                                                                                                                                ccGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGgacg                                                                                                              >  1:338739/1‑183 (MQ=255)                                                                                                                                     ccAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAATCACTGAAACAGTGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGACTAAACTGCGTGCTTATGCTCTTTCTGAACATCTGAAAGAGATCATGGCACGCCTGTTCCAGAAACATATGGTCGACATCATCTCCGTCGAATTCTCTTCCGGTAGGATGGCGGACTGGGCCAACGATGATAAGAAACTGCTGACCt                                      <  1:431073/250‑1 (MQ=255)                                                                                                                                                         gATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGGACGACATCAGCGCCGGCGAATTCTCTTCCGGTATGATGGCGGACTGGGCCAACGATGATAAGAAACTGCTGACCTGGCGt                                 <  1:475938/235‑1 (MQ=255)                                                                                                                                                                                             gAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGc                                                                                                                                                        <  1:13212/80‑1 (MQ=255)                                                                                                                                                                                             gAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGc                                                                                                                                                        >  2:13212/1‑80 (MQ=255)                                                                                                                                                                                                       ggcATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCcccc                                                                                                                                    <  1:242/90‑1 (MQ=255)                                                                                                                                                                                                       ggcATCACCCTGATGATGGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCAcnn                                                                                                                                    >  2:242/1‑88 (MQ=255)                                                                                                                                                                                                                     gatgGACCGTCTCTCTAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGTCATCCCTGTTCCAGAAACATATGGACGACATCATCTCCGGCGAATTCTCTTCCGTTATGATGGCGGACTGTGCCAACGATGATAAGAAACTGCTGTCCTGGCGTGAAGAGACCGGCAAAACCGCGTTTGAAAccn  <  1:52725/206‑2 (MQ=255)                                                                                                                                                                                                                                tctctAATCCGNCGCAACTGCGTGCTTATGCGCTTTCTGANCAGCTGAAAGANATc                                                                                                                                             >  2:76440/1‑56 (MQ=255)                                                                                                                                                                                                                                 ctctAATCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGGACGAAATCATCTACGGCGAATTCTCTTCCGGTATGATGGCGGACTGGGACAACGATGATAAGAAATTGCTGACCTg                                     >  1:503944/1‑159 (MQ=255)                                                                                                                                                                                                                                       |                                                                                                                                                                                            GCGGGTGTGCTGGAATCGTCCTTCGTTGCGGAAGTGAAATCTGACCTGATGGGCGAGCAAACCATCCTGTGCGGTATGTTGCAGGCTGGCTCTCTGCTGTGCTTCGACAAGCTGGTGGAAGAAGGTACCGATCCAGCATACGCAGAAAAACTGATTCAGTTCGGTTGGGAAACCATCACCGAAGCACTGAAACAGGGCGGCATCACCCTGATGATGGACCGTCTCTCTAACCCGGCGAAACTGCGTGCTTATGCGCTTTCTGAACAGCTGAAAGAGATCATGGCACCCCTGTTCCAGAAACATATGGACGACATCATCTCCGGCGAATTCTCTTCCGGTATGATGGCGGACTGGGCCAACGATGATAAGAAACTGCTGACCTGGCGTGAAGAGACCGGCAAAACCGCGTTTGAAACCG  >  NC_000913/3958576‑3958993

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑