Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	1,138,130	C→T	P254S (CCG→TCG)	flgJ →	putative peptidoglycan hydrolase FlgJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	1,138,130	0	C	T	85.7%	59.2 / ‑5.4	28	P254S (CCG→TCG)	flgJ	putative peptidoglycan hydrolase FlgJ
Reads supporting (aligned to +/- strand):  ref base C (0/4);  new base T (14/10);  total (14/14)
Fisher's exact test for biased strand distribution p-value = 9.78e-02
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGATCCTCGCTCAGGCGGCACTGGAATCTGGTTGGGGGCAACGGCAAATCC‑GCCGCGAAAA‑CGGCGAGCCGAGCTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACCCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGCCGATAATACTCTGTAATTGAAGGCTTATAAGGA  >  NC_000913/1137888‑1138371                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                   tGATCCTCGCTCAGGCGGCACTGGAATCTGGTTGGGGGCAACGGCAAATCC‑GCCGCGAAAA‑CGGCGAGCCGAGCTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTAc                                                                                                                                                                                                                                            >  1:376691/1‑251 (MQ=255)        cGCTCAGGCAGCACTGGAATCTGGTTGGGGGCAACGGCAAATCC‑GCCGCGAAAA‑CGGCGAGCCGAGCGATAACCTGTTTGGTGTCCAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGCCTGACTATGAAAACGGAGGAGCGAAGAAAGTTAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGGATAGGGAAACCTAGTAGACGTACCATGAGCTGTTAACGCGTAACTCGCGCGACGcggccg                                                                                                                                                                                                                                     >  2:250113/1‑251 (MQ=255)             aGGCGGCACGGGAATCTGGTTGGGGGCAACGGCAAATCC‑GCCGCGAAAA‑CGGCGAGCCGAGCTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTgacg                                                                                                                                                                                                                                <  1:111439/251‑1 (MQ=255)              ggcggcACTGGAATCTGGTTGGGGGCAACGGCAAATCC‑GCCGCGAAAA‑CGGCGAGCCGAGCTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTgacg                                                                                                                                                                                                                                >  1:492726/1‑250 (MQ=255)                                     ggCAACAGCAAATCCCGCCGGGAAAAACGGAGGGCCGAGCTATAACCTGTTTGGTGTAAAAGCCTCTGG‑CAACTGGAAAGGG‑CCGGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGACGT‑T‑TC‑GCGTCTACAGCT‑CTTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGGGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAgg                                                                                                                                                                                                         <  2:135231/251‑1 (MQ=255)                                          cGGCAAATCC‑GCCGCGAAAA‑CGGCGAGCCGAGCTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGgcgc                                                                                                                                                                                                   >  1:138398/1‑250 (MQ=255)                                                     gacgcgAAAA‑CGACGAGCCGAGCTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAGACGAAGATAGGAAAAGCGAATT‑T‑TC‑TCGTCTACAGCT‑CGCATCTGGACGCCTTGTCGGTTTACGTTGGGCTGTTAACGCGTAACTCAGTCTACGCCGACGTGACGGCCGCCCACAGTGCCGGAAC‑GGAGGCGCAGGcccacca                                                                                                                                                                                         >  2:114987/3‑246 (MQ=255)                                                         ggaaacccggcagccggagttttcaCCTGTTTGGTGTCAAAGCC‑CTGGACAAC‑GGAAAGGGGCCAGTTCCTGAAACCCCCACGACTGAAGAGGAAACCGGCGAAGCGAATAAGGTAAAGGCGAAGT‑T‑CC‑GCTTCTACAGCC‑CGTATCGGGAAGCTTGGTCGGATTACGTGGGGCTGTTAACGCGTACCTCGGTCGACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGAc                                                                                                                                                                                     <  2:149460/227‑1 (MQ=255)                                                                   cgagccgagcTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGCATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGTACGCCGCGCGTGC‑GGACCAGGGTGCGCAGGCCCAACAGGACGCGGGCTATg                                                                                                                                                                           >  2:484074/1‑251 (MQ=255)                                                                     agccgagcTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGcc                                                                                                                                                                         >  1:26266/1‑251 (MQ=255)                                                                       ccgagcTATAACCTGTTGGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCGGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCAc                                                                                                                                                                       <  1:133848/251‑1 (MQ=255)                                                                                      tttGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGCAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTACCGCGTAACTCGCGCTACGCCGCCGGGCCGACCGCCGCGCGTGC‑GGACAAGGGGGCGTAGGCCCTACAGGCCGCGGGCTATGCCCCCGATCCTCACTATGc                                                                                                                                                        >  2:497758/1‑251 (MQ=255)                                                                                                                           aGTTACTGAAATCACCACGAATGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGGGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAAt                                                                                                                     <  1:529204/251‑1 (MQ=255)                                                                                                                                    aaacccccagactgaagaaaaaaaCGGAGAAGCAAAGAAAGTAAA‑G‑GAAGTGTCTC‑GCGTCTACACCT‑CGTCTCTGGAACCCTTGTCGTATTACGTAGGCGGGTTAACGCGTAGCTGGCCCGCCGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACGCACCAACATGATTCAGCAGATGAAATCTATAAGCg                                                                                                            <  2:26266/231‑1 (MQ=255)                                                                                                                                                  aagatGAAAACGGAGAAGCTAAGAAAGAAAAAGCGGA‑T‑T‑TCAGGTTCAAC‑GCTGCGTATCTGGTAGCCTTGTCGGCTTCCGTGGGGTGGTTAACGCGTAACTCGCGCTACGCCGCCGTGCCGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCaaa                                                                                              <  2:205754/248‑1 (MQ=255)                                                                                                                                                       gAAACCGGCGAAGCGAAGAAAGTAAAAGCGAATT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTGAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTa                                                                                         <  1:429588/251‑1 (MQ=255)                                                                                                                                                            cGGCGAAACGCAGCAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCGTGTCGGATTACGTTGGGCTGTTAACGCGAAACTCGAGCTACGCCGCCGTGCCGACCGCCGCGAGTGC‑GGAACAGGGGGCGCATGCCCTACAGGACGAGGGCTATGCCACCGATCCTCACCATGCCCGCAAACTCCCCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGGAAGCAACACCTaaaga                                                                                     >  2:446467/1‑246 (MQ=255)                                                                                                                                                                gaagcaaagAAAGTAAAAGCGAAGT‑T‑TC‑GCGTTTACAGCT‑CGTATCTGGAAGCCTTGCCGGATTACGTTGGGCTGTTAACGCGTAACCCGCGCTACGCCGCCGTGACGACCGCCGCGAGGGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACGATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGaa                                                                                <  1:355496/251‑1 (MQ=255)                                                                                                                                                                 aagcgaagAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACCCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAAc                                                                               <  1:338193/251‑1 (MQ=255)                                                                                                                                                                     gaagaaAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGTCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTg                                                                           >  1:261003/1‑251 (MQ=255)                                                                                                                                                                                     aaGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTTGTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAAt                                                           <  1:133164/251‑1 (MQ=255)                                                                                                                                                                                     aaGT‑T‑TC‑GCGTCTACAGCT‑CGTATATGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTTTGAACATTGATAATCTGATCTGaa                                                            >  2:96749/1‑250 (MQ=255)                                                                                                                                                                                                                  tGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGCCGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTAAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGcc                                  >  2:297956/1‑251 (MQ=255)                                                                                                                                                                                                                   ggAAGCCTGGTCGGAGTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGCCg                                 <  1:520304/251‑1 (MQ=255)                                                                                                                                                                                                                      aGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGCCGat                               >  1:111002/1‑250 (MQ=255)                                                                                                                                                                                                                                  ttACGTTGGGCTGTTAACGCGTAACTCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGCCGATAATACTCTGTAAt                  >  1:183317/1‑251 (MQ=255)                                                                                                                                                                                                                                         gggCTGTGACCGCGTACCCCGCGCTACGCGGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGCCGATAATACTCTGTAATTGAAGGc           <  1:94417/251‑1 (MQ=255)                                                                                                                                                                                                                                                  cgatttAACCCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGCCGATAATACTCTGTAATTGAAGGCTTATAAGGa  <  1:186167/246‑1 (MQ=255)                                                                                                                                                                                                                                                           |                                                                                                                                                                                                                                                   TGATCCTCGCTCAGGCGGCACTGGAATCTGGTTGGGGGCAACGGCAAATCC‑GCCGCGAAAA‑CGGCGAGCCGAGCTATAACCTGTTTGGTGTCAAAGCCTCTGG‑CAACTGGAAAGGG‑CCAGTTACTGAAATCACCACGACTGAATATGAAAACGGCGAAGCGAAGAAAGTAAAAGCGAAGT‑T‑TC‑GCGTCTACAGCT‑CGTATCTGGAAGCCTTGTCGGATTACGTTGGGCTGTTAACGCGTAACCCGCGCTACGCCGCCGTGACGACCGCCGCGAGTGC‑GGAACAGGGGGCGCAGGCCCTACAGGACGCGGGCTATGCCACCGATCCTCACTATGCCCGCAAACTCACCAACATGATTCAGCAGATGAAATCGATAAGCGACAAGGTGAGCAAAACCTACAGTATGAACATTGATAATCTGTTCTGAATAACTCAAGTCCGGCGGGTCGCTGCCGATAATACTCTGTAATTGAAGGCTTATAAGGA  >  NC_000913/1137888‑1138371

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 12 ≤ ATCG/ATCG < 13 ≤ ATCG/ATCG < 26 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑