Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,018,260	(A)8→9	coding (315/444 nt)	fliJ →	flagellar biosynthesis protein FliJ

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,018,252	1	.	A	93.3%	94.0 / ‑0.2	30	coding (307/444 nt)	fliJ	flagellar biosynthesis protein FliJ
Reads supporting (aligned to +/- strand):  ref base . (1/1);  new base A (19/9);  total (20/10)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.58e-01

GAGTGCCGGGATAACCAGCAACCGCTGGATCAACTATCAGCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AG‑‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAGTTCGCCCAGCGCGCCGCCATGAGGAAACCT  >  NC_000913/2018116‑2018383                                                                                                                                            |                                                                                                                                      gAGTGCCGGGATAACCAGCAACCGCTGGATCAACTATCAGCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AG‑‑a‑aa                                                                                                                                  <  1:634990/140‑1 (MQ=255)     gCCGGGATAACCAGCAACCGCTGGATCAACTATCAGCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AG‑‑a‑aaaaaa                                                                                                                              >  1:104534/1‑140 (MQ=255)                 aGCAACCGCTGGATCAACTATCAGCAGTTTACCCATACGATGGAAAAAACCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGc                                                                                                                   <  2:278117/140‑1 (MQ=255)                     aCCGCTGGATCAACTATCAGCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGc                                                                                                               <  1:704615/140‑1 (MQ=255)                         cTGGATCAACTATCAGCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTgg                                                                                                           <  1:784052/140‑1 (MQ=255)                           ggATCAACTATCAGCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCa                                                                                                         <  1:637452/140‑1 (MQ=255)                                       agcagTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGGTGGCG‑AG‑‑ACAAAAAAAAAACGTTTGCAGGCCTGGCAGACACTGCAGGa                                                                                             >  2:322542/1‑140 (MQ=255)                                       agcagTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGCTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGa                                                                                             >  2:676960/1‑140 (MQ=255)                                        gcagTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGaa                                                                                            >  1:665549/1‑140 (MQ=255)                                            tttATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGc                                                                                        >  1:112790/1‑140 (MQ=255)                                               aTCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGAAA‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCaa                                                                                      >  2:718421/1‑140 (MQ=255)                                                      cGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCAcggc                                                                              >  1:523/1‑140 (MQ=255)                                                           gAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGAAA‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCa                                                                          <  1:718421/140‑1 (MQ=255)                                                                   aaagaCTCAGCATCCCCAGCAACTTAATCAGGGGACGAAAAAAGTTGACATTGCCC‑TGAACAGTTGGCGAAA‑‑A‑AAAAAAACAACGTTTGCGGGCCTGGCAGACACTGCAGGACGGGCAATCCACGGCGGCACTGCTTGCa                                                                 <  2:716525/136‑1 (MQ=255)                                                                            gCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGc                                                        >  2:647158/1‑140 (MQ=255)                                                                            gCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGc                                                        >  2:745007/1‑140 (MQ=255)                                                                             cATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGcc                                                       >  1:579524/1‑140 (MQ=255)                                                                             cATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGcc                                                       >  1:765340/1‑140 (MQ=255)                                                                                cGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCg                                                    >  1:829056/1‑140 (MQ=255)                                                                                  ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTctgt                                                  >  1:716525/1‑137 (MQ=255)                                                                                  ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt                                                  <  2:104534/140‑1 (MQ=255)                                                                                  ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt                                                  >  2:50074/1‑140 (MQ=255)                                                                                  ccAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGAt                                                  <  2:523/140‑1 (MQ=255)                                                                                         tttAATCAGGGGAGGAAGAAGGTTGAC‑TTGCCCGTGATCAGTTGGGGAAA‑‑A‑AAAAAAAAAACGTTGGCGGGCCTGGCGAACACGCCAGGAAGGGCAATCCACGGCGGCACTGTTTGCAGAAAACCGCCTCGATCAGaaaa                                           <  2:829056/139‑1 (MQ=255)                                                                                            aaTCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAga                                        <  1:647158/140‑1 (MQ=255)                                                                                                   ggACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGa                                 >  2:708399/1‑140 (MQ=255)                                                                                                    gACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTTCTTGCAGTCAACCGCCACGATGCGAAAAAGATGGATGAg                                >  2:393731/1‑140 (MQ=255)                                                                                                    gACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAg                                >  2:678398/1‑140 (MQ=255)                                                                                                                  aCATTGCCC‑TGAACAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAGTTCGCCCAgcgcgc                  >  1:659270/1‑140 (MQ=255)                                                                                                                              aaCAGTTGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAGTTCGCCCAGCGCGCCGCCATGAGGa       <  2:57856/140‑1 (MQ=255)                                                                                                                                   ttGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAGTTCGCCCAGCGCGCCGCCATGAGGAAACCt  >  2:27865/1‑140 (MQ=255)                                                                                                                                   ttGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAGTTCGCCCAGCGCGCCGCCATGAGGAAACCt  >  1:38782/1‑140 (MQ=255)                                                                                                                                   ttGGCG‑AGA‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAGTTCGCCCAGCGCGCCGCCATGAGGAAACCt  >  1:147649/1‑140 (MQ=255)                                                                                                                                            |                                                                                                                                      GAGTGCCGGGATAACCAGCAACCGCTGGATCAACTATCAGCAGTTTATCCAGACGCTGGAAAAAGCCATTACTCAGCATCGCCAGCAACTTAATCAGTGGACGCAGAAAGTTGACATTGCCC‑TGAACAGTTGGCG‑AG‑‑A‑AAAAAAACAACGTTTGCAGGCCTGGCAGACACTGCAGGAACGGCAATCCACGGCGGCACTGCTTGCAGAAAACCGCCTCGATCAGAAAAAGATGGATGAGTTCGCCCAGCGCGCCGCCATGAGGAAACCT  >  NC_000913/2018116‑2018383

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 15 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑