Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,640,045	+C	coding (13/534 nt)	rrrQ ←	putative lysozyme

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,640,045	1	.	C	95.8%	70.8 / ‑4.2	24	coding (13/534 nt)	rrrQ	putative lysozyme
Reads supporting (aligned to +/- strand):  ref base . (0/1);  new base C (12/11);  total (12/12)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

CACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑T‑TTTTGTGTTCATAGATATTTATGATGAGGACGCTCGTGCTTATTGGCAGGATTTTCAATCTTAAAGGAGTACTGATGCTGCAGATAAGACTCAACTTTTTCTGACAATTTTTCTGCTACTTCCAGGAAGACTTGCCGGACGCTCCTTCTGGCTGCTGCCTCATAAAACTCCAGCGCAGCTCCTTCAACACGGTCCATGGCGACATCCAGGTCAAAAAT  >  NC_000913/1639811‑1640263                                                                                                                                                                                                                                             |                                                                                                                                                                                                                           cACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAccc                                                                                                                                                                                                              <  1:264321‑M1/250‑4 (MQ=255)         aTGGCGTTGCCCTGGTCGCATTTTTCCTGCGACAGTTTCATATTGGGAAAAACGGTGTTTCCGGCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGACCCAGCGCGGTATGCCATGGTGTGGTTACCTGGTGTTTCTTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCGGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCTcccgcccgcttc                                                                                                                                                                                                     <  2:401956‑M1/251‑13 (MQ=255)                                          aGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAAATGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatc                                                                                                                                                                     >  2:393531‑M1/1‑206 (MQ=255)                                                        aaaaaCGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggctcatactgaagctcccc                                                                                                                                                      >  1:39474‑M1/1‑192 (MQ=255)                                                        aaaaaCGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctcccc                                                                                                                                                      <  1:274159‑M1/251‑60 (MQ=255)                                                            aCGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATTTGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑tc                                                                                                                                                                                                                            <  2:7219/177‑2 (MQ=255)                                                            aCGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATTTGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑tc                                                                                                                                                                                                                            >  1:7219/1‑176 (MQ=255)                                                                 ttttcctcccaccactgtggcaCCCCGACAGATGGTCCATATGCCAGAACCAGCGCGGTAGGCCATTGTGTGGTTTCCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATTTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatg                                                                                                                                              <  1:200131‑M1/242‑68 (MQ=255)                                                                    tccatccaCCACTGCAGCACCCCCACCCATGGTCCATATGCCAGAACCATCGCCGTATGCCATTGTGAGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTCTCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGC‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaacattgggatcatactgaatctccccgccagatgcctc                                                                                                                                          >  2:193528‑M1/1‑180 (MQ=255)                                                                          caccacTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtag                                                                                                                                    <  1:393531‑M1/251‑78 (MQ=255)                                                                                     ccccccgaCAGATGTTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgc                                                                                                                         <  2:104387‑M1/249‑89 (MQ=255)                                                                                            aCAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGCGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcctcgcgcgaccttc                                                                                                                  >  2:177262‑M1/1‑156 (MQ=255)                                                                                                    tCCATATGCCAGAACCATCGCGGTATGCCTTTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTAGCTGAGGCGCGGAGGCGCCAGCACCAATCAGCCCCAGAACGGCAGCCGACAGGCCTTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtctgacgatattcatcataaactttgggatcatactgaagctccccgccagatgccgcctgtagacgcatcgcgcgaccttcgggaact                                                                                                           <  2:159506‑M1/250‑103 (MQ=255)                                                                                                                   cATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGACACTGGTCAAGTATCTGAGGAGCAGATGCGCCCGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttccgatattcatcataacctttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagc                                                                                           >  1:436865‑M1/1‑133 (MQ=255)                                                                                                                               ccATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAAGCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGATT‑TTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaa                                                                                <  2:404743‑M1/250‑130 (MQ=255)                                                                                                                                 aTTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGCGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑tc                                                                                                                                                                                                                            >  1:309453/1‑107 (MQ=255)                                                                                                                                 aTTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGGCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑tc                                                                                                                                                                                                                            <  2:309453/108‑2 (MQ=255)                                                                                                                                                   ttttCGTCCAGAACCTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAAAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctgtccagctataaagcgaagccaaacgaatacctgct                                                              <  2:185859‑M1/248‑148 (MQ=255)                                                                                                                                                           cAGAAACTGGTCAAGTCTCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagccgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaagcaaaacgaatacctgctgcttgtgca                                                     >  1:170429‑M1/1‑93 (MQ=255)                                                                                                                                                              aaaCTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaagccaaacgaatacctgctgcttgtgcaagttt                                                >  1:103785‑M1/1‑90 (MQ=255)                                                                                                                                                                   ggTCAAATACCTGACGAGCAGATACGCCAGCCCAAATCACCGCCAGAACGGCACCCGACAGGACGTGTCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggctcatactgaagctccccgccagctgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagagaagccaaacgaataactgctgcttgtgcaagttttgttt                                           >  2:199231‑M1/1‑85 (MQ=255)                                                                                                                                                                     acaAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgctacgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaagccaaacgaatacctgctgcttgtgcaagttttgttttt                                         <  1:429650‑M1/250‑169 (MQ=255)                                                                                                                                                                           aTCTGAGGATCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTGTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaacgttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccatctataaagcgaagccaaacgaataccgtctgcttgtgcaagttttgtttttgaacc                                    <  2:436865‑M1/250‑174 (MQ=255)                                                                                                                                                                             cTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaagccaaacgaatacctgctgcttgtgcaagttttgtttttgaaccga                                  >  2:448020‑M1/1‑75 (MQ=255)                                                                                                                                                                                 ggagCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctcc                                                                                                                                                        <  1:316240‑M1/128‑58 (MQ=255)                                                                                                                                                                                 ggagCAGATGAGCCAGCACAAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGC‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctcc                                                                                                                                                        >  2:316240‑M1/1‑71 (MQ=255)                                                                                                                                                                                  gagCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTAA‑TCTTTTGTGTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaagccaaacgaatacctgctgcttgtgcaagttttgtttttgaaccgaaatac                             >  2:105745‑M1/1‑70 (MQ=255)                                                                                                                                                                                                     aaTCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑TCTTTTGTGTTCAcccgcacgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcatcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaagccaaacgaatccctgctgcttgtgcaagttttgtttttgaaccgaaatcaaaaagagcgtccgctttagg         >  2:124405‑M1/1‑51 (MQ=255)                                                                                                                                                                                                            cccgaaccggcggcctacgggccgtatctga‑tcttttgtgTTCAcccgcccgcttcgtcttacgatattcatcataaactttgggatcatactgaagctccccgccagatgcctcctgtagacgcatcgcgcgaccttcgggaactaaatcccctttccagctataaagcgaagccaaacgaatacctgctgcttgtgcaagttttgtttttgaaccgaaatacaaaagagcgtcagtttgaagcatttaa  <  2:150212‑M1/232‑208 (MQ=255)                                                                                                                                                                                                                                             |                                                                                                                                                                                                                           CACGCTCAATGGCGTTGACCTGGTCGCATTTTTCCTTCGACAGTTTCATATTGGGAAAAACGGTTTTTCCATCCACCACTGTGGCACCCCGACAGATGGTCCATATGCCAGAACCATCGCGGTATGCCATTGTGTGGTTACCTTCTTTTTCGTCCAGAAACTGGTCAAGTATCTGAGGAGCAGATGCGCCAGCACCAATCAGCGCCAGAACGGCAGCCGACAGGCCGTATCTGA‑T‑TTTTGTGTTCATAGATATTTATGATGAGGACGCTCGTGCTTATTGGCAGGATTTTCAATCTTAAAGGAGTACTGATGCTGCAGATAAGACTCAACTTTTTCTGACAATTTTTCTGCTACTTCCAGGAAGACTTGCCGGACGCTCCTTCTGGCTGCTGCCTCATAAAACTCCAGCGCAGCTCCTTCAACACGGTCCATGGCGACATCCAGGTCAAAAAT  >  NC_000913/1639811‑1640263

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑