Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	581,322	C→T	A163A (GCC→GCT)	nohD →	putative DNA‑packaging protein NohD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	581,322	0	C	T	84.4%	47.6 / 5.2	32	A163A (GCC→GCT)	nohD	putative DNA‑packaging protein NohD
Reads supporting (aligned to +/- strand):  ref base C (3/2);  new base T (13/14);  total (16/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 7.83e-01

AGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑CGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACT  >  NC_000913/581123‑581555                                                                                                                                                                                                          |                                                                                                                                                                                                                                           aggaactaaaaaaTGCAAAAGATTCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGAGGATGGCCGGAGACGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTc                                                                                                                                                                                          >  1:77666/9‑250 (MQ=255)            aatgcaaaagattCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTTATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACAGCATTAAAGCCATGAACAAATCAGCTGCGCTGGATGAAATAATACCGTGGTTGCTGAGTGAATATATCGAACAGTCAGGTTaaggggc                                                                                                                                                                              <  1:120193/239‑6 (MQ=255)                  aaagattCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGcagc                                                                                                                                                                        <  1:41001/245‑4 (MQ=2)                      attCCGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTaaggggcttcagcacnc                                                                                                                                                                    <  1:136550/249‑16 (MQ=2)                          cGCTGAGGTGGTGGAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcg                                                                                                                                                                <  1:72937/251‑8 (MQ=2)                              naaGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGACACCCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGaaa                                                                                                                                                                                              >  1:22387/2‑216 (MQ=17)                                 ggggtggAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgg                                                                                                                                                         >  1:159252/3‑237 (MQ=255)                                  tggtggAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcggg                                                                                                                                                        >  1:13835/1‑236 (MQ=255)                                    gtggAAACCGCATTCTGCACGTTCGTGCTGTCGCTGATGGCCGGAGAAGAAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGCCATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgggtc                                                                                                                                                      >  1:39174/1‑234 (MQ=2)                                      ggAAACCGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCAGAGAAGTAGCCAACATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGAGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCCGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgggtct                                                                                                                                                     >  1:98379/1‑232 (MQ=255)                                           ccGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcgggtctactttc                                                                                                                                               <  1:50260/251‑25 (MQ=255)                                           ccGCAGTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATAGTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTGGCGGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCGGCactctgcgctctcgggtcttctttc                                                                                                                                               <  1:135619/251‑25 (MQ=255)                                            cGCATTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTG‑CTGGAGTTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAACACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAACTAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcac                                                                                                                                                                      >  1:94972/1‑226 (MQ=2)                                               aTTCTGCACGTTCGTGCTGTCGCGGATGGCCGGAGAAGTAGCCAGCATTCTTGATGGAG‑TTCCTCTGTCGGTTCAGCGGCGCTTCCCGGAGCTGGAAAACCGACATATTGATCTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCGGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTgcagcactctgcgcgcgcggg                                                                                                                                                        <  1:121768/238‑16 (MQ=255)                                                                                           gTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑CGCGCCGGGCTTCGCTCACTGTTCAgg                                                                                                                                    <  1:50281/213‑1 (MQ=255)                                                                                                                               cgcttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGa                                                             >  1:138083/7‑249 (MQ=255)                                                                                                                                 nttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGACGG‑ACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGGTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGcag                                                                                                                                                                         >  1:103802/5‑138 (MQ=255)                                                                                                                                 nnncccNGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGcac                                                                                                                                                                         <  2:103802/136‑3 (MQ=9)                                                                                                                                      cGGAGCTGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACAGCATGAAAGCCATGAACAAAGCAGCTGCGCGGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGTCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTg                                                    <  1:88546/251‑1 (MQ=255)                                                                                                                                           ntGGAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCCGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGagtcg                                                                        >  1:37707/2‑222 (MQ=9)                                                                                                                                             ggAAAACCGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGCCCAAAGCAGCTGAGCTGGATGAAATCATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTATACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCCGACGATAATTACTATTTACCCAAAGAGTCGGCCTACCAGGACGGGCGCTGGGAAacg                                             >  1:128682/1‑250 (MQ=255)                                                                                                                                                   ccGACATATTGATTTCCTCAA‑GAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAacgttgccg                                       >  1:5438/1‑244 (MQ=255)                                                                                                                                                           ttGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑cgcgn                                                                                                                                                          <  1:109241/128‑2 (MQ=255)                                                                                                                                                           ttGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑Cgcgc                                                                                                                                                          >  2:109241/1‑128 (MQ=255)                                                                                                                                                              gatttcctcaagaaggacatcattAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCaacgcg                             >  1:56285/19‑246 (MQ=255)                                                                                                                                                              gatttcctcaagaaggacatcattAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCT‑TCGCGCGCGGGTCTACTTGCGCTGTACCGACCTGGGTCTCAAACGGCGTTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCGTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCaacgc                              <  1:172111/232‑5 (MQ=255)                                                                                                                                                                       aagaaggtcatcattAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTAAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGTAAACGTTGCCGTTTCAACGCGCGATCATgn                    <  1:105192/242‑2 (MQ=255)                                                                                                                                                                          aaggacatcattAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATg                 <  1:70962/245‑1 (MQ=255)                                                                                                                                                                            ggacatcattAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCCGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATGCg               >  1:12102/5‑251 (MQ=255)                                                                                                                                                                                      aaaGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATGACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATGCGATgggtaac      <  1:162386/250‑5 (MQ=255)                                                                                                                                                                                         nccATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCAGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCCACGCGCGATCATGAATGCGATgggtaacgatt  >  1:140965/2‑243 (MQ=255)                                                                                                                                                                                           cATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGagtcggcctacc                                                                 <  1:134201/186‑12 (MQ=255)                                                                                                                                                                                                          |                                                                                                                                                                                                                                           AGGAGCTGAAAAATGCCAGAGACTCCGCTGAAGTGGTGGAAACCGCATTCTGTACTTTCGTGCTGTCGCGGATCGCAGGTGAAATTGCCAGTATTCTCGACGGGA‑TCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAA‑ACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑CGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACT  >  NC_000913/581123‑581555

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑