Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,740	0	C	A	41.3%	73.3 / 16.3	47	L3I (CTC→ATC)	thrC	L‑threonine synthase
Reads supporting (aligned to +/- strand):  ref base C (10/17);  new base A (19/0);  total (30/17)
Fisher's exact test for biased strand distribution p-value = 5.61e-06
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTC  >  NC_000913/3597‑3889                                                                                                                                                |                                                                                                                                                            tGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTAc                                                                                                                                                        <  2:810721/149‑1 (MQ=255)    tCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATc                                                                                                                                                    <  2:468008/150‑1 (MQ=255)    tCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATc                                                                                                                                                    <  1:505481/150‑1 (MQ=255)           gtgtgACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAg                                                                                                                                              <  2:118299/149‑1 (MQ=255)             gtgACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATc                                                                                                                                           <  2:330300/150‑1 (MQ=255)               gACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATcac                                                                                                                                         <  2:779433/150‑1 (MQ=255)                 cAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTAc                                                                                                                                                        <  2:123581/133‑1 (MQ=255)                       ggAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGGGCACGGGGACTGGGAAAATAAAAGAAAACCTACAATATGTAAGATAACaa                                                                                                                                       >  1:589764/1‑144 (MQ=255)                         aaaCCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGt                                                                                                                             <  1:663698/151‑1 (MQ=255)                           aCCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCa                                                                                                                           <  2:907710/151‑1 (MQ=255)                             cGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCGAGGAATGGGAAAATAAATGAAAATCTACAATCTTAAAGATCACAAAGAGCA‑GGGCa                                                                                                                           >  1:587409/1‑149 (MQ=255)                                  aGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTgc                                                                                                                    <  2:205895/151‑1 (MQ=255)                                     gcgTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGGGGAATTGAAAACCAAATGAAAAACTACAATCTGAAAGAACAAAACGAGCA‑ggggagggtt                                                                                                                      >  1:985869/1‑138 (MQ=255)                                     gcgTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGGAAACTAAAATAAAAACTACAATCTGTAAGATCACAACCAGCA‑GGGCAGCTTTtcg                                                                                                                   >  1:871620/1‑149 (MQ=255)                                          gCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCGAGCACTTGGAAACTAAAAAAAAATACACAAACTTAAAGAACACAAAGAGCA‑GGGTAGCGTTGCGC‑aa                                                                                                               >  2:633211/1‑147 (MQ=255)                                                   ttGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGGGCACCAGGAGTGGAAAAATAAATAAAACTCTACAAACTCGAAGAACACAACCAGAC‑GGGCAGAGTTTCGC‑AAGGC‑CT‑AA‑ccc                                                                                                  >  2:522694/1‑148 (MQ=255)                                                         aaGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGGAAACTAAATGAAAATCTACAAACTGAAAGATCACAACGAGCA‑GGTCAGCTTTTCGC‑AAGCC‑GT‑AA‑ACCAGGGGGTgg                                                                                         >  1:147961/1‑151 (MQ=255)                                                         aaGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGGAAAAAAAAAAAAAATATACAAACTGTAAGAACATAACAAGCA‑GGGCCGCCTTTTGC‑AAGCC‑GT‑AA‑ACACGGGGGTgg                                                                                         >  2:559064/1‑151 (MQ=255)                                                              cTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCGCGGGGACTGGGAAAATAAATAAAAACCTACAAACTGAAAAATCACAACAAGCA‑GGGCAGCTTTGCGG‑AAGCC‑GC‑AACCCCAGGGGTgggg                                                                                        >  1:524298/1‑148 (MQ=255)                                                                       aaaTCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGAATGGGAAACTAAAAGAAACTCTACAATCTGAAAAATCACAAACAGCA‑GGGCCGCGTTTGGC‑AAACC‑GT‑AA‑ACCAGGGGGTGGGG‑CAAAAACAgggg                                                                          >  1:945962/1‑151 (MQ=255)                                                                            aGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGAAAAATAAATTAAAATCTTCAAACTGAAAGAACACAACCAGCA‑GGGCAGCTTTTCGC‑AAGCC‑GT‑AA‑CCCAGGGGGTGGGG‑AAAAAACAggggggggt                                                                     >  1:71434/1‑146 (MQ=255)                                                                              gAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCCCCAGTACTGGAAAACTTAATAAAAATCTACAAACTTAAAGATCACAACAAGCC‑GGGCAGCCTTTCGC‑AACAC‑CT‑AACCCCAGGGGTGGGGA‑AAAAAT‑AGGGGCGGtttt                                                                   >  1:733561/1‑151 (MQ=255)                                                                                  gTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTcc                                                               <  2:559788/151‑1 (MQ=255)                                                                                    tttGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTTGGAAAATAAAAGGAAATCTACAAACTTAAAAATCACAAACAGGA‑GGGCAGCTTTGCGC‑AAACCGGA‑AA‑CCAAGGGGTTGGGA‑AAAAACAAGGGGTGGTTTTTTccc                                                              >  2:788013/1‑150 (MQ=255)                                                                                      tGTTCATATTTGCCGGCTGGATACGGCGGGGGCACGAGTAATGGGAAAATAAATAAAAATCCACAAACTTAAAAATCACAACGAGGA‑GGGCAGCCTTTTGC‑AAGCC‑GT‑AA‑CCCCCGGGGTGGGC‑GAAAAACAGGGGGTGTTTTTTTCGCAc                                                           >  1:132985/1‑151 (MQ=255)                                                                                      tGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCa                                                            <  2:230992/150‑1 (MQ=255)                                                                                        ttCATATTTGCCGGCTGGATACGGCGGGGGCCCGAGAACTGGACAAATAAATTAAATTCTACCATATGGAAGATCCCCACCAGGA‑GGTCAACCTTTAGC‑CAACC‑GT‑AA‑CCCAGGGGTTTGGCGAAAAATCCGGGGGGTTTTTTTctcc                                                             >  1:1001623/1‑145 (MQ=255)                                                                                        ttCATATTTGCCGGCTGGATACGGCGGGGGCACGAGGACTGGGAAAATAAAAGAAAATCTACAATCTGAAAAATCACAACGAGCA‑GGGCCGCTTTGCGC‑AAGCC‑CTAAA‑CCCAGGGGTGGGGC‑AAAAA‑CAGGGGGTGGTTTTTTCCCAc                                                           >  1:775835/1‑149 (MQ=255)                                                                                         tCATATTTGCCGGCTGGATACGGCGGGCGCACGAGGACTGGGAAAAAAAATTAAAAACCAAAATCTTGAAAATCACAACGAGCA‑AGGGAGCTTTTTGCAAAACC‑CA‑AA‑CCCCGGGGTGGGGG‑AAAAACAAGGGGGGGtttttt                                                                 >  2:998345/1‑143 (MQ=255)                                                                                           atatTTGCCGGCTGGATACGGCGGGGGCACGCGGATTTGAAAAAAAAAAAAAACTCTACAATCTTAAAAATAACAACGAACACGGGAGGCCTTGC‑C‑AAAAC‑GT‑AA‑CCCACGGGGTGGGC‑GAAAAAAAAGGGGTGttttttttcccccacac                                                      >  2:883817/1‑140 (MQ=255)                                                                                            tatTTGCCGGCTGGATACGGCGGGCGCCCGAGTAATGGAAAACTAAATGAAAATCTACAAATTGAAAGATCCCAACACGGA‑GGGCCGCTTTTCGC‑AAGCC‑GT‑AA‑CCCCAGGGGTGGGC‑AAAAAACAGGGGGTGGTTTTTTCGCCCCAcc                                                       >  1:973133/1‑149 (MQ=255)                                                                                            tatTTGCCGGCTGGATACGGCGGGCGCCCCAGAAACGGGAAACAAAAATAAAATCTACAATCTGTAAAAAAAAAACACGCA‑AGGGAGCTTTTTGC‑AAAAC‑GTAAA‑CCCCGGGGTGGGCA‑AAAAAACAGGGG‑GGTTTTTTTTGCaccacc                                                       >  2:492636/1‑149 (MQ=255)                                                                                             atTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAAAAAAAATCTACAATATGAAAGATCACAACCAGCA‑GGTCAGCTTTTCGC‑CAGCC‑CT‑AA‑CCCCGGGGGTGGGG‑AAAAAACAGGGGGTGTTTTTTTTGCCCGAcc                                                       >  1:269256/1‑148 (MQ=255)                                                                                               ttGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGcc                                                   <  2:457405/150‑1 (MQ=255)                                                                                                tGCCGGCTGGATACGGCGGGCGCACGAGGAATGGAAAAATAAATGAAAATCCACAAACTGAAAGATCACAACGAGCA‑GGGCAGCTTTTCGC‑AAGCC‑GT‑AA‑CCCAGGGGGTGGGC‑AAAAATCAGGGGGCGTTTTTTTCCCCCCACCCGCCgg                                                 >  1:478038/1‑151 (MQ=255)                                                                                                  ccGGCTGGATACGGCGGGCGGACGAGGACTGGGAAAAAAAAATAAAATCTTAAAACTGGAAGAACACAAAGAGGA‑GGGCAGCCTTGCGC‑AAACC‑CG‑AA‑ACCACGGGGTGGGC‑AAAAAAAAAGGGGGGGTTTTTTTGCCCGACCCGCCgg                                                 >  2:231931/1‑149 (MQ=255)                                                                                                    ggCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAAtt                                             <  2:708268/151‑1 (MQ=255)                                                                                                          aTACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCct                                       >  1:635602/1‑151 (MQ=255)                                                                                                            aCGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCctga                                     <  1:795931/151‑1 (MQ=255)                                                                                                            aCGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCctg                                      <  1:626902/150‑1 (MQ=255)                                                                                                              ggcgggcgCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCctgac                                    >  2:817834/1‑150 (MQ=255)                                                                                                                             aCTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATg                    >  2:421481/1‑151 (MQ=255)                                                                                                                                      ttAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTg           >  2:764414/2‑151 (MQ=255)                                                                                                                                      cTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTg           >  2:419225/1‑151 (MQ=255)                                                                                                                                        aaaTGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTgg          >  1:470426/1‑150 (MQ=255)                                                                                                                                          aTGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGAtt       >  1:253608/1‑151 (MQ=255)                                                                                                                                            gAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGAttt      <  1:256234/150‑1 (MQ=255)                                                                                                                                                ctctACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTc  >  2:39941/1‑150 (MQ=255)                                                                                                                                                |                                                                                                                                                            TGTTCGCTCTGTGTGACAAGCCGGAAACCGCCCAGCGCGTTGCCGACTGGTTGGGTAAGAACTACCTGCAAAATCAGGAAGGTTTTGTTCATATTTGCCGGCTGGATACGGCGGGCGCACGAGTACTGGAAAACTAAATGAAACTCTACAATCTGAAAGATCACAACGAGCA‑GGTCAGCTTTGCGC‑AAGCC‑GT‑AA‑CCCAGGGGTTGGGC‑AAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTGAAGCTGGATTTTGTC  >  NC_000913/3597‑3889

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑