Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,781,152	0	A	G	21.1%	142.0 / 13.0	76	intergenic (+135/‑63)	lldD/trmL	L‑lactate dehydrogenase, FMN‑linked/tRNA Leu mC34,mU34 2'‑O‑methyltransferase, SAM‑dependent
Reads supporting (aligned to +/- strand):  ref base A (40/20);  new base G (0/16);  total (40/36)
Fisher's exact test for biased strand distribution p-value = 6.75e-07
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCC  >  NC_000913/3781053‑3781249                                                                                                      |                                                                                                  gggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGa                                                                                                   >  1:275336/1‑100 (MQ=255)  ggAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAg                                                                                                  >  1:446457/1‑100 (MQ=255)   gagaGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAgg                                                                                                 <  2:1759270/100‑1 (MQ=255)     gagGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAgggg                                                                                               >  1:1356057/1‑100 (MQ=255)          gACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAg                                                                                          <  2:1356048/100‑1 (MQ=255)          gACCGTTCGGCGCTGTATGTACACCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAg                                                                                          >  2:1188625/1‑100 (MQ=255)           aCCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAgg                                                                                         <  1:540593/100‑1 (MQ=255)             cGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGcc                                                                                       >  1:1841484/1‑100 (MQ=255)              gTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCACCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCg                                                                                      >  2:505035/1‑100 (MQ=255)                  ggCGCTGTCTGTACTCCCTCCCTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCCCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCAc                                                                                   <  2:1708083/99‑1 (MQ=255)                        gtatgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCAc                                                                            >  2:791961/1‑100 (MQ=255)                         tatgtaCTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCAcc                                                                           >  1:694631/1‑100 (MQ=255)                                 ccccccctcgGAAACGACCCGGCCCTCTTTTTTTCCCCCGCCCCCCCCGGGGGGGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                   <  2:1417639/94‑1 (MQ=255)                                 cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                   >  1:1426786/1‑100 (MQ=255)                                 cccTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                   >  1:1586572/1‑100 (MQ=255)                                 cccTCACCCTGAAACGACCCCGCGCTCTTTTTTTCCCCCTCCCCCCCCCGGGGAGGGGCC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCt                                                                   <  2:1450476/100‑1 (MQ=255)                                  cctccctcTCAACCGACCCCGCACTTTTTTTTTCTCCCTCCCCCCTCGGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTg                                                                  <  2:1421716/100‑1 (MQ=37)                                   cTCACTCGGAACCCCCCCCCCCCTCTTTTTTCCCCCCCCCCCCCCCGGGGGGGGGGGC‑G‑GGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                                 <  1:1978489/100‑1 (MQ=255)                                     cACTCTAAAACGACCCCGCCCTTTTTTTTCCCCCCTCGCCCCCCGGGGGAGGGGGC‑G‑GGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTa                                                               <  1:1816293/100‑1 (MQ=255)                                      cctctAAAACCACCCCGCACTCTTTTTTTCCCCCTCGCCCCCCCGGGGAGAGGGC‑C‑GGGGGGAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTAt                                                              <  2:1665929/99‑1 (MQ=37)                                      aCTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTAt                                                              >  2:993535/1‑100 (MQ=255)                                       ntctGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATc                                                             >  1:604232/2‑100 (MQ=255)                                       ctctAAAAGGACCCCGCCCTTTTTTTTTCCCCCTCGCCCC‑CCGGGGGGGGGGC‑CGGGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGc                                                                 <  2:1841468/96‑1 (MQ=255)                                        tctGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATcc                                                            >  2:705580/1‑100 (MQ=255)                                         ctGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCt                                                           >  1:260673/1‑100 (MQ=255)                                           gAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGc                                                         >  1:1169208/1‑100 (MQ=255)                                            aaaCGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGcc                                                        >  2:495007/1‑100 (MQ=255)                                            aaaCGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGAGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGcc                                                        >  1:1235169/1‑100 (MQ=255)                                            aaaCCACACCGCACTCTTTTTTCCTCCCCCCCCCCGCCGGGGAGAGGGC‑C‑GGGGGGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATcc                                                            <  1:1756565/96‑1 (MQ=255)                                               cGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGccccc                                                     >  1:257004/1‑100 (MQ=255)                                                    ccGCCCTTTTTTTTTCCCCCCCGCCCC‑CCGGGGGGGGGGCGG‑GGGGCGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCCGCCCCCGc                                                   <  2:1507334/97‑1 (MQ=255)                                                      gCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTaa                                              >  1:2001801/1‑100 (MQ=255)                                                         ctctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggg                                           >  1:873073/1‑100 (MQ=255)                                                         ctctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGCCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggg                                           >  2:121450/1‑100 (MQ=255)                                                           ttttttttCCCCCCCCCCCCGCGGGGGAGAGGGC‑G‑GGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTa                                               <  2:1200238/93‑1 (MQ=255)                                                           ctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                                         >  2:1767383/1‑100 (MQ=255)                                                           ctTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAggggg                                         >  2:1968191/1‑100 (MQ=255)                                                               ttttCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGt                                     >  2:1937848/1‑100 (MQ=255)                                                                tttCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTa                                    >  1:1292069/1‑100 (MQ=255)                                                                tttCCCCCTCCCCCCTCCGGGGGGGGGCC‑C‑GGGGTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCan                                      <  2:1265552/98‑2 (MQ=255)                                                                atcttcCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTa                                    <  1:691067/96‑1 (MQ=255)                                                                   ctcCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGc                                 >  1:1452238/1‑100 (MQ=255)                                                                   ccccccccccccTCCGGGGAGGGGGC‑G‑GGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATg                                  <  1:908032/91‑1 (MQ=255)                                                                    tcCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTaagat                                >  2:691065/1‑96 (MQ=255)                                                                    cccccCGCCCCTCCGGGGCGGGGGC‑G‑GCGGTGAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATg                                  <  1:446792/97‑1 (MQ=255)                                                                      ccTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaa                              >  2:324889/1‑100 (MQ=255)                                                                       cTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaaa                             >  1:12398/1‑100 (MQ=255)                                                                         cGCCCCTCGGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTaan                             <  2:604230/98‑2 (MQ=255)                                                                          gCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGAAAAAGGCCCCACTGCTCACCAATGTTCTGCTGTCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAAc                            >  2:2016821/1‑98 (MQ=255)                                                                             cccccGGGGGGAGGCC‑G‑GGGGGAAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                       <  1:705582/97‑1 (MQ=255)                                                                             ccTCGGGGGAGAGGGC‑G‑GGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                       <  2:122053/100‑1 (MQ=255)                                                                             ccTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGt                       >  2:1580220/1‑100 (MQ=255)                                                                              ccccGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTa                      <  2:1611810/98‑1 (MQ=255)                                                                              cTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTa                      >  2:598364/1‑100 (MQ=255)                                                                              cTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTa                      >  2:442042/1‑100 (MQ=255)                                                                              cTCCGGGGAGAGGAC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTa                      >  2:1703814/1‑100 (MQ=255)                                                                               tCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTAc                     >  2:288965/1‑100 (MQ=255)                                                                                cgggggggggggC‑G‑GGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTAc                     <  1:1477678/97‑1 (MQ=255)                                                                                cgggggAGGGGGC‑C‑GGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACt                    <  2:41509/98‑1 (MQ=255)                                                                                ccGGGGAGAGGGC‑C‑GGGGTGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACt                    <  2:873070/100‑1 (MQ=255)                                                                                   gggAGAGGGC‑G‑GGGGTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTa                 <  1:993539/100‑1 (MQ=255)                                                                                   gggAGAGGCC‑C‑GGTGTGAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACttt                  <  2:446456/99‑1 (MQ=255)                                                                                    ggggggggC‑G‑GGGGGGGGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAc                <  1:1188631/95‑1 (MQ=255)                                                                                    ggAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAc                <  2:257003/100‑1 (MQ=255)                                                                                    ggAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTAc                <  2:814277/100‑1 (MQ=255)                                                                                        agGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAc            >  1:156281/1‑100 (MQ=255)                                                                                         gggC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGa              <  2:1169202/97‑1 (MQ=255)                                                                                         gggC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAAcc           >  1:461288/1‑100 (MQ=255)                                                                                         gggC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGACAGTATGCTAAACATCGTACTTTACGAAcc           >  2:622882/1‑100 (MQ=255)                                                                                           gC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAg         >  2:532126/1‑100 (MQ=255)                                                                                            c‑c‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGa        >  2:649344/1‑100 (MQ=255)                                                                                                ggggTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCTTACTTTACGAACCAGaaa      <  1:121451/100‑1 (MQ=255)                                                                                                ggggTGGGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGaa       <  2:2001783/99‑1 (MQ=255)                                                                                                ggggTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAg         <  2:1235163/97‑1 (MQ=255)                                                                                                  ggTGAGGGAAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAAt     <  2:694629/99‑1 (MQ=255)                                                                                                    tGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTcc  >  2:546595/1‑100 (MQ=255)                                                                                                    ggAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTcc  <  1:755936/99‑1 (MQ=255)                                                                                                      |                                                                                                  GGGAGAGGGGACCGTTCGGCGCTGTATGTACTCCCTCACTCTGAAACGACACCGCACTCTTTTTTTCTCCCTCGCCCCTCCGGGGAGAGGGC‑C‑GGGGTGAGGGGAAAAGGCCGCACTGCTCACCAATTTTCTGCTATCCTGCCCCCGCACTAAGGGGGCAGTATGCTAAACATCGTACTTTACGAACCAGAAATTCC  >  NC_000913/3781053‑3781249

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑