Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,649,971	C→T	P60S (CCG→TCG)	ydfD →	lysis protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,649,971	0	C	T	96.0%	68.5 / NA	25	P60S (CCG→TCG)	ydfD	lysis protein
Reads supporting (aligned to +/- strand):  ref base C (0/0);  major base T (11/13);  minor base G (0/1);  total (11/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.87e-01

CTATTAAATAAAATATGCATTGTTTCAATGCTGGCTCGTTTACGTCTGATGCCAAAAGGATGTGCACAATGAATTCAGCATTTGTGCTTGTTCTGACAGTTTTTCTTGTTTCCGGAGAGCCAGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCCCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCG  >  NC_000913/1649726‑1650187                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                         cTATTAAATAAAATATGCATTGTTTCAATGCTGGCTCGTTTACGTCTGCAGCCAAAAGGATGTGAACACTGAATTAAGAATTTGAGCTTGTTCTGACAGTTTTTCTTGTTTCAGGAAAGCCCGTTAATATTGCGGTCAGTGTTCAACGGACAATGCAGGAGTGTATGACTGCAACAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGc                                                                                                                                                                                                                      >  1:416138/1‑250 (MQ=255)                                                                   caATGAATTCAGCATTTGTGCTTGTTCTGACAGTTTTTCTTGTTTCCGGAGAGCCAGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGAtt                                                                                                                                                   >  1:249054/1‑251 (MQ=255)                                                                   caATGAATTCAGCATTTGTGCTTGTTCTGACAGTTTTTCTTGTTTCCGGAGAGCCAGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGGCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCg                                                                                                                                                                                                  <  1:335688/204‑1 (MQ=255)                                                                                aTTTGTGCTTGTTCTGACAGTTTTTCTTGTTTCCGGAGAGCCAGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCAtn                                                                                                                                           <  1:130003/246‑2 (MQ=255)                                                                                                      nnnnnnnnnnccNNNNNGCCNGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTc                                                                                                                                                                                                                 <  2:283149/144‑1 (MQ=255)                                                                                                            gTTTCCGGAGAGCCCGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGt                                                                                                          >  1:123741/1‑251 (MQ=255)                                                                                                                          aGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTGTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTg                                                                                            <  1:396945/251‑1 (MQ=255)                                                                                                                          aGNNNNNATTNCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAg                                                                                                                                                                                                       <  2:272957/144‑1 (MQ=255)                                                                                                                                       gtcagtGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGCTAATATCGAAATCTCGGCAGGGCTTTAAAACAg                                                                                                                                                                                                       >  1:258232/1‑131 (MQ=255)                                                                                                                                               tCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGaan                                                                        <  1:84670/250‑2 (MQ=255)                                                                                                                                                 acaGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGAACTgg                                                                     >  1:60874/1‑251 (MQ=255)                                                                                                                                                                              gcaACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGATGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAgg                                                             <  1:257788/230‑1 (MQ=255)                                                                                                                                                                              gcaACCGAACAGAAAATCCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCGCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCt                                                                                                                                         <  1:381609/154‑1 (MQ=255)                                                                                                                                                                                  ccGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTNTTCNCCAGNATNATATCGAAATCTCGGNAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATCCTTNNANNNCNGCAATGGc                                                                                                                                                          <  2:312489/133‑1 (MQ=255)                                                                                                                                                                                  ccGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATCCTTATATGCCAGCAATGGc                                                                                                                                                          >  1:312489/1‑133 (MQ=255)                                                                                                                                                                                         gAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTAACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTAATCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCAt                             >  1:368340/1‑251 (MQ=255)                                                                                                                                                                                                   ggTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAAGCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTgc                                                                                           <  1:287462/179‑1 (MQ=255)                                                                                                                                                                                                      aaCTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCGGTAGCCACAGCCATTGAAGCTGGcgan                <  1:116125/251‑2 (MQ=255)                                                                                                                                                                                                                   tCGATAAAGTTATTCACCAGGATAATATAGAAATCTCGGCAGGTCTTTAAAACAGTTTCGTAATCAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAAc                                                                                                                  >  1:406887/1‑140 (MQ=255)                                                                                                                                                                                                                    nnntAANGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACa                                                                                                                 <  2:265322/137‑1 (MQ=255)                                                                                                                                                                                                                    ngATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACa                                                                                                                 >  1:265322/2‑140 (MQ=255)                                                                                                                                                                                                                    cGATAAAGTTATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTcn  <  1:110248/251‑2 (MQ=255)                                                                                                                                                                                                                            ttATTCACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAggn                                                    <  1:48701/193‑2 (MQ=255)                                                                                                                                                                                                                                 cACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACCGTTCCGTAATAAATATCCGCTTTCCTTCTTATATGCCCGCCATGGCAGGGCTTTGTTCCTCCTTAAATCTGTCATGCGGTTCAAACACATGAGTAACGTCTTTATTTGCGCCGCTATTCCTGACGAAc                                                                        >  1:302911/1‑168 (MQ=255)                                                                                                                                                                                                                                 cACCAGGATAATATCGAAATCTCGGCAGGTCTTTAAAACAGTTCCGTAATACATATCCGGTTTCCTTCTTATATGCCAg                                                                                                                                                                 >  1:77426/1‑79 (MQ=255)                                                                                                                                                                                                                                                      |                                                                                                                                                                                                                         CTATTAAATAAAATATGCATTGTTTCAATGCTGGCTCGTTTACGTCTGATGCCAAAAGGATGTGCACAATGAATTCAGCATTTGTGCTTGTTCTGACAGTTTTTCTTGTTTCCGGAGAGCCAGTTGATATTGCAGTCAGTGTTCACAGGACAATGCAGGAGTGTATGACTGCAGCAACCGAACAGAAAATTCCCGGTAACTGTTACCCGGTCGATAAAGTTATTCACCAGGATAATATCGAAATCCCGGCAGGTCTTTAAAACAGTTCCGTAATAAATATCCGGTTTCATTCTTATATGCCAGCAATGGCAGGGATTTGTTCATCCTTAAATCTGTCATGAGGTTAAAACAAATGAGTAAAGTCTTTATTTGCGCCGCTATTCCTGACGAACTGGCAACAAGGGAAGAAGGCGCTGTGGCTGTAGCCACAGCCATTGAAGCTGGCGACGAACGCCGTGCTCG  >  NC_000913/1649726‑1650187

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 20 ≤ ATCG/ATCG < 35 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑