Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,413,735	0	A	T	40.9%	59.2 / 26.6	44	Y2* (TAT→TAA)	ydaC	DUF1187 family protein, Rac prophage; putative double‑strand break reduction protein
Reads supporting (aligned to +/- strand):  ref base A (0/26);  new base T (18/0);  total (18/26)
Fisher's exact test for biased strand distribution p-value = 9.71e-13
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413594‑1413885                                                                                                                                              |                                                                                                                                                       tACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAAtt                                                                                                                                                  >  1:25820/1‑147 (MQ=255)   cTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTTATTTTTTACATTaa                                                                                                                                                >  1:733188/1‑148 (MQ=255)     ttCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTATATGaa                                                                                                                                                >  2:185456/1‑146 (MQ=255)      tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTtttaaaatgcagcctc                                                                                                                                          >  2:114963/1‑139 (MQ=255)      tCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCt                                                                                                                                           <  2:248919/150‑1 (MQ=255)          ctctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTCATGGATACcccc                                                                                                                                         >  1:225208/1‑148 (MQ=255)          ctctctGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTcc                                                                                                                                         <  1:475599/148‑1 (MQ=255)                ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattattatt                                                                                                                                <  2:87880/151‑1 (MQ=255)                ggAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCattatta                                                                                                                                  <  1:221188/149‑1 (MQ=255)                 gAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTAttt                                                                                                                               <  2:514378/151‑1 (MQ=255)                 gAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTAttt                                                                                                                               <  2:501389/151‑1 (MQ=255)                     cGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTGATTTTTTACACTAACACCCCCCTTCtttttt                                                                                                                               >  2:527539/1‑147 (MQ=255)                             tcttTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCg                                                                                                                    <  1:304453/150‑1 (MQ=255)                                tttttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGtt                                                                                                                  <  2:269382/149‑1 (MQ=255)                                  tttACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTAATAAAACCCCCCTTATTTTTTTCCGTGGGTTGtttttt                                                                                                              >  2:93378/1‑151 (MQ=255)                                    tACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTc                                                                                                             <  2:160344/150‑1 (MQ=255)                                    tACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTc                                                                                                             <  2:703469/150‑1 (MQ=255)                                      ccTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCAt                                                                                                          <  2:676081/151‑1 (MQ=255)                                             gCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACATTAACACCCCCCTTATTATTTTCAGTGGTTTGTTTTTTTCCTCttt                                                                                                      >  2:24749/1‑148 (MQ=255)                                             gCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCg                                                                                                    <  1:383520/150‑1 (MQ=255)                                               aTTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAGTATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGt                                                                                                 <  2:287285/151‑1 (MQ=255)                                                        cATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCtttt                                                                                        <  1:55605/151‑1 (MQ=255)                                                         aTTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATAAAAACCCCCCCTTTTTTTTTTCGTGGTTTGTTTTTTTCCTCTTTTTTGTGCTTCttttt                                                                                       >  1:76982/1‑151 (MQ=255)                                                             tGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTACAATAACAACCCCATTTTTTTTTTCAGTGGGTTGTTTTTTTCATTTTTTTTGTGGttttttttt                                                                                      >  2:688025/1‑147 (MQ=255)                                                               aTTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTc                                                                                 <  1:96390/151‑1 (MQ=255)                                                                      tAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCAt                                                                           <  1:659488/150‑1 (MQ=255)                                                                        gTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAATGAAAACCCCCCTTTTTATTTTCAGTGGGTCGTTTTTTTCCTCTTTCGGGGGGTTCTTTTTTACTTTCACCCTaa                                                                         >  2:579759/1‑150 (MQ=255)                                                                          ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTTATGAAAACCCCCCCTTTTATTTTCCATGGGTTGTTTTTTTCATTTTTTGAGTTGTTTTTTTTTTCTTTCCCCAAAAcc                                                                       >  1:676864/1‑150 (MQ=255)                                                                          ttAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAAcc                                                                       <  2:340894/150‑1 (MQ=255)                                                                            aGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAAATTTTTTTAAGAACACCTCCCTTTTTTTTTTCCGTGGGTTGTTTTTTTCATCTTTTTTGTGGTTCTTTTTTTCTTCCCCCCTaaaccg                                                                     >  2:317225/1‑146 (MQ=255)                                                                                        tCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTTAATGAAAACCTCCCTTTTTTTTTTCAGTGGGTCGTTTTTTTCCTCTTTCTGGTGCTTCTTTTTTTTTTCCTCCATAACCGGTTCGGGAtt                                                            >  1:763945/1‑147 (MQ=255)                                                                                            gTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTTTAAATGAACACCCCCCCTATTATTTCCAGTGGTTCGGTTATTTCCTCTTTCTAGTGGTTCTTTTTCACTTCCCACAAAAACCGTTCGGGAGTCGCa                                                        >  2:216137/1‑147 (MQ=255)                                                                                             tCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATcc                                                     <  2:632031/149‑1 (MQ=255)                                                                                                          aGTGCCACCTTCCTTTTCAATAGTGGCGGGAATTTTTTATATGAAAACCCCCCTTTTTTTTTTCCGTGGGTTGTTTTTTTTTTCTTTTTAGTGCTTCTTTTTTTCTTTCCCCCTAACCGGTTTGGGGTTTGCATCCGTTTCTCtt                                            >  1:143582/1‑145 (MQ=255)                                                                                                                aCCTTCCTTTTCAATAGTGGCGGGAAATTTTTACATTAACACCTCCCTTTTTTTTTTCAGTGGGTTGTTTTTTTTATCTTTTTAGTGCTTTTTTTTTTCTTCCACCCTAACCGGTTCGGGGTTTGCATCCCTTTCACTTTCCTCCGTAat                                 >  1:697032/1‑150 (MQ=255)                                                                                                                 ccttccttTTCAATAGTGGCGGTAATTTTTTTCATTAAAACCCCCCCTTTTTTTTTCACTGGGTTGTTTTTTTCTTCTTTTGAGTGCTTTTTTTTTTCTTTCACCCCAAACCGTTTGGGGTTTGCCTCCCTTTCACtt                                            >  1:203446/1‑138 (MQ=255)                                                                                                                  cttccttTTCAATAGTGGCGGTAATTTTTTATAATAACACCCCCCTTATTTTTTTCAGTGGTTTGTTTTTTTCCTCTTTTTAGTGGTTTTTTTTTTCTTTCCCCCTAACCCGTTCGGGGTTCGCATCCCTTACACTTTCCTCCGGAata                                >  2:291934/1‑149 (MQ=255)                                                                                                                    tccttTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATc                              <  2:320215/149‑1 (MQ=255)                                                                                                                     ccttTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCt                            <  1:684778/150‑1 (MQ=255)                                                                                                                          tCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAAt                       <  2:936965/150‑1 (MQ=255)                                                                                                                          tCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAAt                       <  2:649138/150‑1 (MQ=255)                                                                                                                            aaTAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATGACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGc                    <  1:297073/151‑1 (MQ=255)                                                                                                                                    cGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCg            <  2:84548/151‑1 (MQ=255)                                                                                                                                        aaTTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTa         <  1:416489/150‑1 (MQ=255)                                                                                                                                           tttATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTg      <  1:185392/150‑1 (MQ=255)                                                                                                                                             tataCATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGAt    <  1:887989/150‑1 (MQ=255)                                                                                                                                              ataCATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATgg  <  2:344642/151‑1 (MQ=255)                                                                                                                                              |                                                                                                                                                       TACTTTCTGCTCTCTGGAAACGCCTGCTTCTTTTTTACCTGAGAGCATTTTTTCGCATTCTGATTTCGTTAGTTTAGATTTTGAATATCTTGTCCAGTTAGTAGGAGTGCCACCTTCCTTTTCAATAGTGGCGGTAATTTTATACATGAACACCTCCATTATTATTTCCAGTGGTTCGTTTATTCCATCTTTCGAGTGCTTCTTTTTCACTTCCACCATAACCGGTTCGGGATTCGCATCCGTTACACTTCGCTCGGTAATATCCTGAAATGGCTTTCACCGTTACTGATGG  >  NC_000913/1413594‑1413885

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 17 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑