Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	436,500	0	G	T	40.9%	67.5 / 17.6	44	P289P (CCG→CCT)	thiL	thiamine monophosphate kinase
Reads supporting (aligned to +/- strand):  ref base G (15/11);  new base T (0/18);  total (15/29)
Fisher's exact test for biased strand distribution p-value = 4.61e-05
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.69e-01

GATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCG  >  NC_000913/436360‑436648                                                                                                                                             |                                                                                                                                                       gATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGt                                                                                                                                               >  2:654774/1‑150 (MQ=255) gATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGt                                                                                                                                               >  1:319076/1‑150 (MQ=255)    gcgcTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCg                                                                                                                                           <  2:740229/151‑1 (MQ=255)         ttCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑a                                                                                                                                      <  2:553188/150‑1 (MQ=255)               ccATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGAct                                                                                                                              <  2:248414/151‑2 (MQ=255)                cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGAccg                                                                                                                             <  2:683877/151‑1 (MQ=255)                cATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGAccg                                                                                                                             <  2:598766/151‑1 (MQ=255)                     tGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGa                                                                                                                         <  1:690472/150‑1 (MQ=255)                       aaCCGGCACAGGCGCTGCGCTGGGGGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGGACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGatat                                                                                                                      >  1:38825/1‑151 (MQ=255)                       aaCCGGAACGGGCGCTGCGCGGGGCGCTCTCTGGGGGTGAAGATTACGATTTGTTTTTCACTGCGCCGGAACTGAACGGTGGCGCGGGGGATGTGGCTCCCGCACACCTGGGCGTACCGTTTACCTGTACCGGGA‑AAA‑TGACCGCCGatat                                                                                                                      <  1:21414/151‑1 (MQ=255)                         ccGGAACAGGCGCTGCGCTGGGGGCTCTCGGGCGGTGAAGATTACGAGTTGTTTTTCGCGGTGCCGGACCTGACCCGGGGCGCGCTGGATGTGGCTCTCGGACCCGGGGGCGTACCTTTTACCTGTGTGGGGA‑AAA‑TGACCGCCGATATc                                                                                                                     <  1:175164/150‑1 (MQ=255)                         ccGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCg                                                                                                                    >  2:23771/1‑151 (MQ=255)                          cGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCg                                                                                                                    >  1:596041/1‑150 (MQ=255)                                 ggCGCTGCGGGGGGCGCTCTCGGGCGGTGAATATTACGTTTTGTTTTTCACTGTGCGGGAACTGACCCGGGGCGCTTGGGTTGTGGCTCTCGGACCCGTGGGCGTACCTTTTACCTGTCCCGGGC‑AAA‑TGCCCGCCGATATCGAAGGGCtt                                                                                                            <  1:211736/151‑1 (MQ=255)                                  gcgctgcgcgGGGCGCTCTCTGGGGGTGAAGATTACGAGTTGTTTTTCCCTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACCCCGGGGCGTCCCGTTTACCTGTATCGGGA‑AAA‑TGACCGCCGATATCGAAGGGCttt                                                                                                           <  2:666315/151‑1 (MQ=255)                                            ggtccctctggggCGGTAAAGTTTAGTATTTGTTTTTCCCTGTCCCGAAAATAACCCGGGGCGGGGTGGTTGTGGCTCTCGGACCCCTGGGTTTCCGTTTTGCCTTTGTCGGAA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCg                                                                                                 <  2:314953/140‑1 (MQ=255)                                                  tctcgGGGGGTTATGTTTGCGAGTTGTGTTCCGTTGCGCCGGAACGAAACGGTGGCGCGGGGGGTTTGCCTCCCGCACACCTGGCGCTACTGTTTCCTTAAACTGGTC‑AAA‑GGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTg                                                                                               <  2:599395/147‑1 (MQ=255)                                                          ggTGAAGTTTCGGATTTTTGTTCCGCTGGGCCGGACCTGCCCCTCGGCGGGCTGGATGTGGCTCCCGCCCCCTTGGGCTTATGTTTTTCATGTACGGGGC‑AAA‑GGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTg                                                                                   <  2:733937/151‑1 (MQ=255)                                                            tGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGtt                                                                                 >  2:174816/1‑151 (MQ=255)                                                                       aGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTg                                                                      >  2:248900/1‑151 (MQ=255)                                                                         ttGTTTTCCCCTGTCCCGAAACTCACCCGTGGCGGGGTGGATGTGGCTCGCGGCCACGGGGGCGTCCTTTTTACCTGTTTGGGGA‑AAA‑GGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAg                                                                          <  1:174493/145‑1 (MQ=255)                                                                          tgtgTTTCTCTGTGCCGGATTTGACCGGTGGCGCGTTGGATGTTGCTCCGGTACCCTTGGGCGTCCTGTTTACCTGTGTGGGGA‑AAA‑TGCCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAg                                                                          <  1:723111/144‑1 (MQ=255)                                                                           gtgtTTCCCTGTGCCGGAACTGACCCGGGGCGCGTTGGGTGTGCCTCTCGGACACCTGGGCGTCCCTTTTACCTTTTTCGGGA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                   <  2:113053/150‑1 (MQ=255)                                                                            tgtTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGaa                                                                   >  2:428335/1‑149 (MQ=255)                                                                             ttttCCCGGTGCGGAAACTGAACGGGGGCGCGCTGGTTGGGCCTTGCGCACGCGGGGGCATCCAGTTTTCCTGTGCCGGGA‑AAA‑AGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAg                                                                 <  2:452208/149‑1 (MQ=255)                                                                                 cACTGTGCCGGAACTGACCGGGGGCGCGCTGGATGTGGCTCTCGGACACCGGGGCTTCCCTTTTCCCTGTATCGGGA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGata                                                             <  2:331223/150‑1 (MQ=255)                                                                                     gggcgggAACAGACCGGGGGCGCGCTGGGTGTGGCTCCGGGCCCCCGGGGCGTCCTTTTTACCTGTTGCGGAA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGAc                                                         <  1:324928/145‑1 (MQ=255)                                                                                          ggaccggAACGGTGGCGGGTTGGGTGTGGCGCTCGGCCCCGTGGGGGTCCCTTTTTCCGGTCGGGGGA‑AAA‑GGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAt                                                      <  1:202670/142‑1 (MQ=255)                                                                                          ggAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCAtttt                                                   >  2:188892/1‑151 (MQ=255)                                                                                           gAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTg                                                  >  2:171030/1‑151 (MQ=255)                                                                                            aaCTGACCGGTGGCGCGTGGGAGGTGGCTCGCGGACACGGGGGCGTCCTTTTTCCTTGTAGCGGAA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGc                                                 <  1:248900/151‑1 (MQ=255)                                                                                            aaCTGACCGGTGGCGCGGTGGATGTGGCTCTCGGCCCCCGGGGCGTCCCTTTTCCCTGTACCGGAA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGatat                                                            <  2:50966/140‑1 (MQ=255)                                                                                                         cgcgcTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATaa                                       >  1:177770/1‑148 (MQ=255)                                                                                                               ggttgtgGCTCTGGGACCCGGGGGCTTCCCTTTTCCCTGTATGGGGA‑AAA‑GGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGAt                                   <  2:460693/143‑1 (MQ=255)                                                                                                               ggttgggcctccCGGCCCCCTGGGGGTCCCTTTTCCTTTTTTGGGGA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATa                                        <  2:121343/133‑1 (MQ=255)                                                                                                               ggATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgc                              >  1:218931/1‑151 (MQ=255)                                                                                                                     ggCTCTGGGACCCGGGGGCTTCCCTTTTCCTTTTATGGGGA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgcg                             <  2:319077/146‑1 (MQ=255)                                                                                                                     ggCCCTGGGACGCGTGGGCTTACTTTTTCCTTGTAGGGGAC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTcgcg                             <  1:608353/146‑1 (MQ=255)                                                                                                                          tcGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGcc                   >  2:647659/1‑151 (MQ=255)                                                                                                                           cggaaccgtGGGTGTACTTTTTCCTTGTAGCGGAA‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGcc                   <  1:87633/142‑1 (MQ=255)                                                                                                                              accccggggCGTACCTTTTTCCCTTTGCGGGCAAAA‑GGGCCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGc                    <  1:588586/141‑1 (MQ=255)                                                                                                                               ccccggggCGTCCCTTTTCCCTTTAT‑GGGC‑AAAGTGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGc                    <  2:639222/140‑1 (MQ=255)                                                                                                                                        gTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAAt     >  2:452910/1‑151 (MQ=255)                                                                                                                                            cGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCg  >  1:442328/1‑150 (MQ=255)                                                                                                                                             |                                                                                                                                                       GATGCGCTTTCTCGCCATGTTGAACCGGAACAGGCGCTGCGCTGGGCGCTCTCTGGCGGTGAAGATTACGAGTTGTGTTTCACTGTGCCGGAACTGAACCGTGGCGCGCTGGATGTGGCTCTCGGACACCTGGGCGTACCGTTTACCTGTATCGGGC‑AAA‑TGACCGCCGATATCGAAGGGCTTTGTTTTATTCGTGACGGCGAACCTGTTACATTAGACTGGAAAGGATATGACCATTTTGCCACGCCATAAAGATGTCGCGAAAAGTCGCCTGAAGATGAGTAATCCG  >  NC_000913/436360‑436648

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑