Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	581,392	T→C	intergenic (+13/‑142)	nohD → / → tfaD	putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	581,392	0	T	C	84.6%	57.2 / 2.7	26	intergenic (+13/‑142)	nohD/tfaD	putative DNA‑packaging protein NohD/putative tail fiber assembly protein TfaD
Reads supporting (aligned to +/- strand):  ref base T (1/3);  new base C (9/13);  total (10/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.16e-01

GTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑CGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTC  >  NC_000913/581213‑581601                                                                                                                                                                                    |                                                                                                                                                                                                                   gTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑CGCGCCGGGCTTCGCTCACTGTTCAgg                                                                                                                                                                                  <  1:50281/213‑1 (MQ=255)                                    cgcttcccGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGa                                                                                                           >  1:138083/7‑249 (MQ=255)                                           cGGAGCTGGAAAACCGACATATTGATTTCCTCAAGAAGGACAGCATGAAAGCCATGAACAAAGCAGCTGCGCGGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGTCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTg                                                                                                  <  1:88546/251‑1 (MQ=255)                                                ntGGAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCCGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGagtcg                                                                                                                      >  1:37707/2‑222 (MQ=9)                                                  ggAAAACCGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGCCCAAAGCAGCTGAGCTGGATGAAATCATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTATACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCCGACGATAATTACTATTTACCCAAAGAGTCGGCCTACCAGGACGGGCGCTGGGAAacg                                                                                           >  1:128682/1‑250 (MQ=255)                                                        ccGACATATTGATTTCCTCAAGAAGGACATCATTAAAGCCATGAACAAAGCAGCTGCGCTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAacgttgccg                                                                                     >  1:5438/1‑244 (MQ=255)                                                                ttGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑cgcgn                                                                                                                                                                                                        <  1:109241/128‑2 (MQ=255)                                                                ttGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑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)                                                                                                                  cTGGATGAAATAATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAAGGGGCAGACGAGAATTACTATCGCCCCAAAGAGTCGTCCTACCAGGGAGGGCGCTGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATGCGATg                                                          <  1:115158/220‑1 (MQ=255)                                                                                                                       tgaaataaTACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCaacn                                                                             <  1:35877/189‑4 (MQ=255)                                                                                                                             aaTACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAATGGCGCTGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATGCGATGGGTAACGATTACATACGTGAGGTCAACGTTGTTAAGTCTGc                 <  1:167903/249‑1 (MQ=255)                                                                                                                                 ncGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGGTGCCGTTTCAACGCGCGATCATGAATGCGATggggaaa                                                    >  1:34213/2‑207 (MQ=255)                                                                                                                                 ccGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTggn                                                                                                <  1:104537/167‑2 (MQ=255)                                                                                                                                  cGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCGGCGGCATTTTGGC‑CGCGCCGGGCTTCGCTCACTGGTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCAGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCGGGGAAACACTGCCCTGTCAGCGGGGCATCAGGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCgtgt           <  1:94806/251‑1 (MQ=255)                                                                                                                                    gggTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATGCGATGGGTAACGATTACATACGTGAGGTCAACGTTGTTAAGTCTGCCCgtgttn         <  1:103057/251‑3 (MQ=255)                                                                                                                                      gTTGCTGAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGagtcggc                                                                                                                    >  1:61100/1‑136 (MQ=255)                                                                                                                                            gAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAATGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATGCGATGGTTAACGATTACATACGTGAGGTCAACGTTGTTAAGTCTGCCCgtgttgtctattc  <  1:120634/250‑10 (MQ=255)                                                                                                                                            gAGTGAATATATCGAACAGTCAGGTTAAGGGGCTGCAGCACTCTGCG‑CGCGCGGGTCTACTTTCGCTGTACCGACCTGAGCCGCAAACGGCGGTTGAAGGGGCAGACGATAATTACTATCTCCCCAAAGAGTCGGCCTACCAGGAAGGGCGCTGGGAAACGTTGCCGTTTCAACGCGCGATCATGAATGCGATGGGTAACGATTACATTCGTTAGGTCAACGTTTTTAAGTCTGCCCGTGTTGGCTAtt   <  1:158885/249‑1 (MQ=255)                                                                                                                                                                                    |                                                                                                                                                                                                                   GTATTCTCGACGGGATCCCCCTGTCGGTGCAGCGGCGTTTTCCGGAACTGGAAAACCGACATGTTGATTTCCTGAAACGGGATATCATCAAAGCCATGAACAAAGCAGCCGCGCTGGATGAACTGATACCGGGGTTGCTGAGTGAATATATCGAACAGTCAGGTTAACAGGCTGCGGCATTTTGTC‑CGCGCCGGGCTTCGCTCACTGTTCAGGCCGGAGCCACAGACCGCCGTTGAATGGGCGGATGCTAATTACTATCTCCCGAAAGAATCCGCATACCAGGAAGGGCGCTGGGAAACACTGCCCTTTCAGCGGGCCATCATGAATGCGATGGGCAGCGACTACATCCGTGAGGTGAATGTGGTGAAGTCTGCCCGTGTCGGTTATTC  >  NC_000913/581213‑581601

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: ‑