Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,284,909	0	T	C	20.4%	92.5 / 17.3	44	F178F (TTT→TTC)	yejM	essential inner membrane DUF3413 domain‑containing protein; lipid A production and membrane permeability factor
Reads supporting (aligned to +/- strand):  ref base T (17/18);  new base C (2/7);  total (19/25)
Fisher's exact test for biased strand distribution p-value = 2.60e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ATTGCTTGAACTGGTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCTTTCGTAC  >  NC_000913/2284813‑2285005                                                                                                 |                                                                                                 attGCTTGAACTGGTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTAtttatc                                                                                               <  1:1006607/100‑1 (MQ=255)    gCTTGAACTGGTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTAttcatcgcc                                                                                            <  2:397447/100‑1 (MQ=255)     cTTGAACTGGTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTAtttatcgcct                                                                                           <  1:852093/100‑1 (MQ=255)     cTTGAACTGGTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTAtttatcgcct                                                                                           >  1:1466139/1‑100 (MQ=255)       tGAACTGGTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTAtttatcgccttt                                                                                         >  1:1389187/1‑100 (MQ=255)             ggTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTAtttatcgcctttatcgcc                                                                                   >  1:311479/1‑100 (MQ=255)                gtTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCg                                                                                >  2:1080063/1‑100 (MQ=255)                 tttGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGc                                                                               <  1:1396956/100‑1 (MQ=255)                     cGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCAtgt                                                                           <  2:642079/100‑1 (MQ=255)                         gTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATgtggtg                                                                       <  2:1422306/100‑1 (MQ=255)                          tGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGgtgt                                                                      <  2:115886/100‑1 (MQ=255)                          tGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGgtgt                                                                      <  1:1370809/100‑1 (MQ=255)                           ggAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGta                                                                     <  1:659061/100‑1 (MQ=255)                             aGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGtata                                                                   <  1:226173/100‑1 (MQ=255)                                 ggCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTg                                                               <  2:11015/100‑1 (MQ=255)                                 ggCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTg                                                               >  2:1501696/1‑100 (MQ=255)                                 ggCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTg                                                               >  1:269833/1‑100 (MQ=255)                                 ggCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTg                                                               >  1:83692/1‑100 (MQ=255)                                  gCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTgg                                                              >  1:651914/1‑100 (MQ=255)                                   cAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTggg                                                             >  1:1031098/1‑100 (MQ=255)                                     aaaGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGcc                                                           <  1:123443/100‑1 (MQ=255)                                          tGCGGAGCTTGACTCGTATTCGACGCTCCGCGCGCCCCCTGTCCTTATTCTTATTCATCGCCATTGTCGCCTCGCATGTGGTGTATATCTGAGCCGATg                                                       <  2:1237260/99‑1 (MQ=255)                                           gcgcAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGcc                                                     >  1:180489/1‑100 (MQ=255)                                           gcgcAGCCTGACGCGTCGTCGACGCTTCACGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGTGCCTATGcc                                                     >  2:1450708/1‑100 (MQ=255)                                               aGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACt                                                 <  2:526743/100‑1 (MQ=255)                                                gCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACt                                                 >  1:491741/1‑99 (MQ=255)                                                 ccTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTc                                               <  1:937800/100‑1 (MQ=255)                                                  cTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATACCAACTTCt                                              <  1:733704/100‑1 (MQ=255)                                                      cgcgTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCg                                          >  1:500592/1‑100 (MQ=255)                                                      cgcgTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCg                                          >  1:1076582/1‑100 (MQ=255)                                                        cgtcgtCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGcc                                        <  1:1127700/100‑1 (MQ=255)                                                         gtcgtcGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGccc                                       <  2:1558614/100‑1 (MQ=255)                                                         gtcgtcGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGccc                                       <  1:74701/100‑1 (MQ=255)                                                         gtcgtcGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGccc                                       >  1:1226146/1‑100 (MQ=255)                                                          tcgtcgACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCg                                      <  2:154123/100‑1 (MQ=255)                                                           cgtcgACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGa                                     >  2:1443750/1‑100 (MQ=255)                                                           cgtcgACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGa                                     >  1:1300843/1‑100 (MQ=255)                                                           cgtcgACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGa                                     >  1:759879/1‑100 (MQ=255)                                                             tcgACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATc                                   <  1:1443758/100‑1 (MQ=255)                                                             tcgACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATc                                   <  2:185952/100‑1 (MQ=255)                                                               gACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCAc                                 <  1:221688/100‑1 (MQ=255)                                                                 cGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCa                               <  2:363327/100‑1 (MQ=255)                                                                    ttCGCGCGCCCGCTGGCCGCATTCTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGc                            <  1:1307918/100‑1 (MQ=255)                                                                            cccGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCt                    <  1:1080069/100‑1 (MQ=255)                                                                              cGCTGGCCGCATTCTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCGAACTTCTATCGCCCGATCACCATGCAGCGCGCTa                   >  2:231760/1‑99 (MQ=255)                                                                                  ggCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTg              >  2:50053/1‑100 (MQ=255)                                                                                  ggCCGCATTCTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTg              <  1:320082/100‑1 (MQ=255)                                                                                         ttCTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCttt       <  1:1215249/100‑1 (MQ=255)                                                                                           cTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCTTTCg     >  2:1481149/1‑100 (MQ=255)                                                                                           cTTATTCATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCTTTCg     >  1:103705/1‑100 (MQ=255)                                                                                            ttatttatCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCCCCATGCAGCGCGCTAACCTGCCGCTTTctt    >  2:703931/1‑98 (MQ=255)                                                                                            ttatttatCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCTTTCGt    >  2:72451/1‑100 (MQ=255)                                                                                             tatttatCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGCTCACCATGCAGCGCGCTAACCTGCCGCTTTCGt    >  2:1568990/1‑99 (MQ=255)                                                                                              atttatCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCTTTCGTAc  <  2:500591/100‑1 (MQ=255)                                                                                              atttatCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCTTTCGTAc  >  2:132245/1‑100 (MQ=255)                                                                                              atttatCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGATAACCTGCCGCTTTCGTAc  >  1:118304/1‑100 (MQ=255)                                                                                                 |                                                                                                 ATTGCTTGAACTGGTGTTTGCGACGTGGAGCTGGCAAAAGCTGCGCAGCCTGACGCGTCGTCGACGCTTCGCGCGCCCGCTGGCCGCATTCTTATTTATCGCCTTTATCGCCTCGCATGTGGTGTATATCTGGGCCGATGCCAACTTCTATCGCCCGATCACCATGCAGCGCGCTAACCTGCCGCTTTCGTAC  >  NC_000913/2284813‑2285005

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 22 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 41 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑