Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP009273	2,145,108	G→A	22.4%	R148K (AGA→AAA)	yegJ →	uncharacterized protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP009273	2,145,108	0	G	A	22.4%	84.8 / 6.4	48	R148K (AGA→AAA)	yegJ	uncharacterized protein
Reads supporting (aligned to +/- strand):  ref base G (12/25);  new base A (9/2);  total (21/27)
Fisher's exact test for biased strand distribution p-value = 5.58e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

ACAAACGTAGAATATGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTACCGCCGGGC  >  CP009273/2144963‑2145256                                                                                                                                                   |                                                                                                                                                       aCAAACGTAGAATATGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGc                                                                                                                                                     <  1:532865/149‑1 (MQ=255)  cAAACGTAGAATATGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑a                                                                                                                                                   <  2:975402/149‑1 (MQ=255)     aCGTAGAATATGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTTTACCACTGATATCTTTTTTGGTTCCCCA‑CCACAAAAAGAAGACCGCGAGCTAAAAGC‑aaaa                                                                                                                                                >  2:1036122/1‑149 (MQ=255)       gTAGAATATGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTTAT‑TCCTTTTTTGTTACCCATCCCAAAAAAAAAACCGAAGAGGCAAAAGG‑aaaaat                                                                                                                                              >  1:811828/1‑147 (MQ=255)          gAATATGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGGTATAACATTTAT‑CCTTTTTTTTTTTCCTATCCCAAAAAAAAAAACGACGAGATAAGAGC‑AAAAATAAtt                                                                                                                                          >  2:642574/1‑150 (MQ=255)            atatGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑Cg                                                                                                                                       <  2:50347/150‑1 (MQ=255)             tatGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGc                                                                                                                                      <  2:135545/150‑1 (MQ=255)              atGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATTCCAATTAT‑CCTTTTTTTTTTACCTATCCAAAAAAAAAAAACGACGAGCTAAGAGC‑AAAAATAATT‑TGc                                                                                                                                      >  2:460977/1‑149 (MQ=255)                 gCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAAt                                                                                                                                  <  2:799355/150‑1 (MQ=255)                    aGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAg                                                                                                                               <  2:486787/150‑1 (MQ=255)                         tGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATAACCTTTAT‑CCTTTTTTTGTTACCTATCCCAAAAAAAAAACCGACGAGCTAAGAGC‑AAAAATAATT‑TGCTTATCAACCGtt                                                                                                                          >  1:779760/1‑150 (MQ=255)                              aaTCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTTTAACATTTAT‑CCTTTTTTTGTCACCTATCCCAAAAAAAAAGCCGACGAGCTAAAAGC‑AAAAATAGTT‑TGCTAATCAGCCGTTAtatt                                                                                                                     >  1:245548/1‑150 (MQ=255)                              aaTCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATAACATTTAT‑TCTTTTTTTTGCACCCATCCAAAAAAAAAAACCGACGAGCTAAAAGC‑AAAATTAATT‑TACTTATTAGCCGCTTtatt                                                                                                                     >  1:814277/1‑150 (MQ=255)                                tCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTTTAACACTGAT‑CCTTTTTTTGTCTCCTATCCCAAAAAAAAAACCGACGAGCAAAAAAC‑AAAAAAAAAT‑CTCTAATCAGCCGCTAtattta                                                                                                                   >  2:992287/1‑150 (MQ=255)                                    gaaagaaGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTTAT‑TCTTTTTTTGTTACCCATCCCAAAGAAAAAAACGACGGGCTAAAAGC‑AAAAATAGTT‑TGCTAATCAACCGTTATATTTTTTGt                                                                                                               >  2:102628/1‑150 (MQ=255)                                          agaTATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTTTAACATTGAT‑TCTTTTTTTGTTACCTATTCCAAAAAAAAAAACGACGAGCCAAAAACAAAAATTTATT‑C‑CTTATCAACCGGTATATTTTTTTTTTtaa                                                                                                          >  2:132770/1‑149 (MQ=255)                                            atatTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATTACCTTTTT‑CCTTTTTTTGTTACCTCACCCAAAAAAGAAAACGCCCAGCCAAAAGC‑AAAAATAATT‑CGCTTATCAACCCTTTTTTTTTTTTTTTtaaatt                                                                                                       >  1:489260/1‑147 (MQ=255)                                                ttCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCCTTTAT‑CCTTTTTTTGTTCCCCATCCCAAAAAAGAAGACGACGAGCTAAAAGC‑AAAAATAGTT‑CGCTAATCAGCCCTTATTTTTTTTTTTTtaaattgggg                                                                                                   >  1:704043/1‑143 (MQ=255)                                                  cAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGt                                                                                                  <  1:212426/149‑1 (MQ=255)                                                   aGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGtt                                                                                                 <  2:196814/149‑1 (MQ=255)                                                               taCGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCt                                                                                     <  2:226758/149‑1 (MQ=255)                                                                 cgcgcgGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTc                                                                                   <  2:357555/149‑1 (MQ=255)                                                                 cgcgcgGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTc                                                                                   <  1:460977/149‑1 (MQ=255)                                                                 cgcgcgGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTCa                                                                                  <  2:64725/150‑1 (MQ=255)                                                                            aaaaTTTACGGCGTTTATACTTTTGTT‑CTTTTATTGGTCCCCTACCAAAAAAAAGAGCCCGACGAGCAAAGAGA‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTTTTAAAACTGGCGTTTGATTTGTTTTCTTCAACCGCCATgag                                                                       <  2:166270/150‑1 (MQ=255)                                                                                     ggcggTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGGTTAATTTTTTTTTTTAAACCCCCTTAGAAaatcccc                                                              >  2:118204/1‑147 (MQ=255)                                                                                         tttATCCCATTGAT‑CTTTTATTGGTCACCTACCAAAAAAAAGAAGCCGACGAGCAAAGAAA‑AAAATTAGTT‑CGCTAACCAGCCTTTTTATTTATTGTTTAACCGGGGGGTTAAATTTTTGTCTTCAACCGCCATGAGAAACTCACTCTGc                                                          <  2:663361/149‑1 (MQ=255)                                                                                               catttGAT‑CTTTTATTGTTCCCCTATCAAAAAAAAGAAGCCGACGAGATAAGAAA‑AAAATTAGTC‑CGTTAATCAGCCTTTATTTTTTTTTTTAAACCGGGGGGTTGATTTTTTGTTTTCAACCGCCATGAGAAACTCACTCTGCCcaca                                                     <  2:774961/146‑1 (MQ=255)                                                                                                    gAT‑CTTTTATTGGTCCCCTATCCAAAAAAAGACGCCGACGAGCTAAGAGA‑AAAATTAGTC‑CGCTAATCAGCCGTTATATTTATTGTTTAACCGGGCGGTTGAATTGTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGcc                                                <  1:102628/149‑1 (MQ=255)                                                                                                    gAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTCAACCGCCATGAGAAAATCACTCTGCCCACAgcgc                                                 >  1:565754/1‑148 (MQ=255)                                                                                                        ccTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAggg                                            >  1:712955/1‑148 (MQ=255)                                                                                                                  cccccTATCAAAAAGAAGAAGCCGACGAGCAAAGAGA‑AAAATTAGTT‑CGCTAATCAGCCTTTATATTTATTTTTAAAACTGGCGGTTGATTTGTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGtttt                                  <  2:245548/147‑1 (MQ=255)                                                                                                                         acaaaaaGAAAAACCCGACGAGTAAAAAGA‑AAATTTAGTC‑CGATAAACAGCCTTTATTTTTATTTTTTAACCGGGGGGTTGAATTGTTTTCTCCAGCCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTatcatca                           <  2:663824/147‑1 (MQ=255)                                                                                                                          ccAAAAGAAGAAGCCGACGAGCTAAGAGA‑AAAATTATTT‑CGTTAATCAGCCTTTATATTTATTTTTTAAACTGGCGGTTGAATTTTTTTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTatcatcat                          <  1:829749/150‑1 (MQ=255)                                                                                                                          caaaaaGAAGAAGCGGACGAACAAAGAAA‑AAATTTTGTT‑CGTTAACCAGCTTTTATTTTTATTGTTAAAACGGGGGGTTGATTTTTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTatcatcat                          <  2:489260/148‑1 (MQ=255)                                                                                                                           aaaaaGAAGAACCCGACGAGCTAAGAGA‑AAAATTAGTT‑CGCTAATCAGCCTTTATATTTTTTTTTTAAACGGGCGTTTAATTTTTTTTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTatcatcat                          <  1:149539/148‑1 (MQ=255)                                                                                                                                gaaaaacCCGACGAGATAAAAGA‑AAATTTAGTC‑CGCTAATCACCATTTATATTTATTGTTTAAACTGGCGTTAGAATTGTTGTCTTCACCCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTAc                    <  1:646792/150‑1 (MQ=255)                                                                                                                                aaagaagCGGACGAGCAAAGAGA‑AAAATTGTTT‑CGCAAATCGCCTGTTATTTTTTTTTTTTAACCGGGCGGTTAATTTTTTTTCTTAAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTAc                    <  1:992287/149‑1 (MQ=255)                                                                                                                                  agaagCCGGAGAGCGAAGA‑T‑AAAAGTAGTTGCGTTATCCAGCGTTTATTTTTGTTGTTAAACCGGGCGGTAGAATTTTTTTCAGAAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGc                  <  2:631923/150‑1 (MQ=255)                                                                                                                                        cgacgaGCTAAGAGA‑AAAATTATTC‑CGCTAATCAGCCTTTATATTTTTTTTTTAAACTGGCGGTTAAATTGTTTTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGttt            <  1:642574/150‑1 (MQ=255)                                                                                                                                         gacgaGCTAAGAGA‑AAAATTGTTT‑CTCTAATCACCTTTTTTATTTTTTTTTTAACCGGGCGTTTGAATTGTTTTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTa           <  1:36835/150‑1 (MQ=255)                                                                                                                                            gaGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTTAATTGTTGTCTTCAACCCCCATGAGAAACTCACTCTGCCCCCAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTAccg        >  2:882312/1‑150 (MQ=255)                                                                                                                                              gCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTTTTTTCTTCAACCGCCATGAGAAAATTACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCCCGTTTAccgcc      >  2:472712/1‑150 (MQ=255)                                                                                                                                              gCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTTTTCCACCGCCCAGAGGAACCCACTTTTCCCCCATCGCCAGTGCCAACGTTTTATCATCCTCCGTACGCTCGTTTAccgcc      >  1:899895/1‑150 (MQ=255)                                                                                                                                               cTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTAcccccg     >  1:171240/1‑150 (MQ=255)                                                                                                                                                tAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTACCGCCgg    >  1:134061/1‑150 (MQ=255)                                                                                                                                                aaaGAGA‑AAAATTATTT‑CGATAATCAGCCTTTATATTTTTTTTTAAAACGGGGGGTTAATTTTTTGTCTTAAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTACCGCCgg    <  1:215826/149‑1 (MQ=255)                                                                                                                                                 aaGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTTTTTTCTTCAACCGCCCTGAGAAACTCACTCTTCCCCCAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTACCGCCggg   >  2:234226/1‑150 (MQ=255)                                                                                                                                                  agagC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTTTCTTCAACCGCCATGAGAAACTCACTCTCCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCCCGTTTACCCCCCGGc  >  1:763101/1‑150 (MQ=255)                                                                                                                                                   |                                                                                                                                                       ACAAACGTAGAATATGGCCAGGAGTGGAAAATCAAGAAAGAAGATATTTCAGACTGGATGTATACGCGCGGGGATAAAATTTACGGCGGTTATACCATTGAT‑CCTTTATTGGTCACCTATCCAAAAGAAGAAGCCGACGAGCTAAGAGC‑AAAATTAGTT‑CGCTAATCAGCCGTTATATTTATTGTTTAAACTGGCGGTTGAATTGTTGTCTTCAACCGCCATGAGAAACTCACTCTGCCCACAGCGCCAGTGCCAACGTTTTATCATCATCCGTACGCTCGTTTACCGCCGGGC  >  CP009273/2144963‑2145256

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑